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

Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

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...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

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...
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

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 characterized.
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the addition of a...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...

You might also read

Related Articles

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

Sort by
Same author

Modeling Chickpea Productivity with Artificial Image Objects and Convolutional Neural Network.

Plants (Basel, Switzerland)·2024
Same author

Quality Control of Human Pluripotent Stem Cell Colonies by Computational Image Analysis Using Convolutional Neural Networks.

International journal of molecular sciences·2023
Same author

Modeling of Flowering Time in <i>Vigna radiata</i> with Artificial Image Objects, Convolutional Neural Network and Random Forest.

Plants (Basel, Switzerland)·2022
Same author

A dual role for DNA binding by Runt in activation and repression of <i>sloppy paired</i> transcription.

Molecular biology of the cell·2021
Same author

Dynamical climatic model for time to flowering in Vigna radiata.

BMC plant biology·2020
Same author

Non-linear regression models for time to flowering in wild chickpea combine genetic and climatic factors.

BMC plant biology·2019
Same journal

Battle royale optimizer for multilevel image thresholding.

The Journal of supercomputing·2025
Same journal

MOBRO: multi-objective battle royale optimizer.

The Journal of supercomputing·2025
Same journal

Optimizing inference of segmentation on high-resolution images in MLExchange.

The Journal of supercomputing·2025
Same journal

Topic sentiment analysis based on deep neural network using document embedding technique.

The Journal of supercomputing·2023
Same journal

AEGA: enhanced feature selection based on ANOVA and extended genetic algorithm for online customer review analysis.

The Journal of supercomputing·2023
Same journal

A Fechner multiscale local descriptor for face recognition.

The Journal of supercomputing·2023
See all related articles

Related Experiment Video

Updated: May 26, 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

DEEP-differential evolution entirely parallel method for gene regulatory networks.

Konstantin Kozlov1, Alexander Samsonov

  • 1Department of Computational Biology, State Polytechnical University, St. Petersburg, 195251, Russia, kozlov@spbcas.ru.

The Journal of Supercomputing
|January 7, 2012
PubMed
Summary
This summary is machine-generated.

We enhanced the Differential Evolution Entirely Parallel (DEEP) algorithm for biological data fitting. A novel migration strategy speeds up convergence for complex gene regulatory network analysis in Drosophila development.

More Related Videos

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
03:08

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Published on: October 3, 2025

An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
11:36

An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Published on: April 21, 2023

Related Experiment Videos

Last Updated: May 26, 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

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
03:08

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Published on: October 3, 2025

An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
11:36

An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Published on: April 21, 2023

Area of Science:

  • Computational Biology
  • Systems Biology
  • Developmental Biology

Background:

  • Biological data fitting is crucial for understanding complex biological systems.
  • Accurate modeling of gene regulatory networks requires efficient computational methods.
  • Existing algorithms may face challenges in speed and convergence for large datasets.

Purpose of the Study:

  • To introduce and evaluate a novel migration scheme for the Differential Evolution Entirely Parallel (DEEP) algorithm.
  • To enhance the speed of convergence in biological data fitting problems.
  • To apply the improved DEEP method to analyze gene regulatory interactions in Drosophila development.

Main Methods:

  • Implementation of a new migration scheme in the DEEP algorithm, where the best individual replaces the oldest in the next branch.
  • Definition of individual 'age' based on survival without changes over iterations.
  • Application of the algorithm to fit parameters of nonlinear differential equations to experimental data for Drosophila gap gene networks.
  • Utilizing a ring topology for computational node networks.

Main Results:

  • The developed DEEP algorithm with the new migration scheme demonstrates high speed of convergence.
  • The algorithm successfully determined parameters for nonlinear differential equations modeling Drosophila gap gene networks.
  • Performance and efficiency were analyzed on a relevant biological test problem.

Conclusions:

  • The enhanced DEEP algorithm offers an efficient approach for biological data fitting.
  • The novel migration strategy significantly improves convergence speed.
  • This method provides a valuable tool for elucidating gene regulatory interactions in developmental processes.