Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Protein Networks02:26

Protein Networks

4.7K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.7K
Protein Networks02:26

Protein Networks

2.9K
No description available
2.9K
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

8.2K
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
8.2K
Gene Conversion02:08

Gene Conversion

10.9K
Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
10.9K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

8.4K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
8.4K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

3.8K
No description available
3.8K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Oxidative stress pathways in noncancerous human liver tissue to predict hepatocellular carcinoma recurrence: a prospective, multicenter study.

Hepatology (Baltimore, Md.)·2011
Same author

Transthiocarbamoylation of proteins by thiolated isothiocyanates.

The Journal of biological chemistry·2011
Same author

Stabilized high-accuracy correction of ocular aberrations with liquid crystal on silicon spatial light modulator in adaptive optics retinal imaging system.

Optics express·2011
Same author

Carcinogenesis of intraductal papillary mucinous neoplasm of the pancreas: loss of microRNA-101 promotes overexpression of histone methyltransferase EZH2.

Annals of surgical oncology·2011
Same author

Clinical significance of UNC5B expression in colorectal cancer.

International journal of oncology·2011
Same author

Antitumor and anti-invasive effects of diverse musk-fragrant macrocyclic ketones and their enhancement by hyperthermia.

Molecular medicine reports·2011

Related Experiment Video

Updated: Mar 29, 2026

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
10:44

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

2.7K

Hub-centered gene network reconstruction using automatic relevance determination.

Matthias Böck1, Soichi Ogishima, Hiroshi Tanaka

  • 1ViroQuant Research Group Modeling, University of Heidelberg, BioQuant BQ26, Heidelberg, Germany.

Plos One
|May 10, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces a new method for reconstructing gene regulatory networks by identifying key hub genes. The approach uses a hierarchical Bayesian model to improve network inference and pinpoint important regulatory interactions from experimental data.

More Related Videos

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

3.7K
Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences
11:25

Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences

Published on: February 11, 2019

8.6K

Related Experiment Videos

Last Updated: Mar 29, 2026

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
10:44

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

2.7K
JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

3.7K
Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences
11:25

Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences

Published on: February 11, 2019

8.6K

Area of Science:

  • Computational Biology
  • Systems Biology
  • Bioinformatics

Background:

  • Biological network inference is challenging due to combinatorial complexity.
  • Existing methods often use constraints to manage complexity.
  • Gene regulatory networks frequently feature a few highly influential hub genes.

Purpose of the Study:

  • To develop a novel method for inferring gene regulatory networks by exploiting topological properties.
  • To specifically identify influential hub genes within these networks.
  • To improve the accuracy and efficiency of biological network reconstruction.

Main Methods:

  • Utilized a Bayesian network model with discrete, Boolean nodes.
  • Employed a hierarchical prior to regularize edge weights and identify hub genes.
  • Performed network reconstruction via posterior distribution maximization or sampling.

Main Results:

  • Successfully reconstructed key regulatory interactions in simulated and real data.
  • Demonstrated superior performance in identifying hub genes compared to state-of-the-art methods.
  • Identified several main hub genes in a large dataset of cell cycle regulated genes.

Conclusions:

  • The proposed method effectively reconstructs biological networks and identifies crucial hub genes.
  • This approach offers a valuable tool for discovering candidate genes for further biological investigation.
  • The developed regularization techniques may advance future network reconstruction methodologies.