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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...
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...
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.
Mutation, Gene Flow, and Genetic Drift01:09

Mutation, Gene Flow, and Genetic Drift

In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).Mechanisms of Genetic VariationThe original sources of genetic variation are mutations,...
Synteny and Evolution02:31

Synteny and Evolution

John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral chromosome underwent...

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Related Experiment Video

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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Published on: February 3, 2023

Reverse engineering a gene network using an asynchronous parallel evolution strategy.

Luke Jostins1, Johannes Jaeger

  • 1Laboratory for Development & Evolution, University Museum of Zoology, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK.

BMC Systems Biology
|March 4, 2010
PubMed
Summary
This summary is machine-generated.

A new parallel island Evolutionary Strategy (piES) algorithm significantly outperforms the parallel Lam Simulated Annealing (pLSA) algorithm for gene regulatory network inference. The asynchronous piES offers substantial speed-ups and improved reliability for complex biological modeling.

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Related Experiment Videos

Last Updated: Jun 15, 2026

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Area of Science:

  • Computational Biology
  • Systems Biology
  • Bioinformatics

Background:

  • Gene regulatory network inference is crucial for understanding cellular processes.
  • Mathematical modeling of gene expression data requires advanced global optimization techniques.
  • Existing methods like parallel Lam Simulated Annealing (pLSA) face challenges with increasing model complexity.

Purpose of the Study:

  • To develop and evaluate a parallel island Evolutionary Strategy (piES) for gene regulatory network inference.
  • To compare the performance of piES against established algorithms like pLSA.
  • To assess the effectiveness of synchronous and asynchronous piES versions.

Main Methods:

  • Implementation of synchronous and asynchronous piES algorithms.
  • Application to a real-world reverse engineering problem: inferring parameters in the gap gene network.
  • Comparison of piES and pLSA based on time to reach specific residual error levels.

Main Results:

  • Asynchronous piES demonstrates minimal communication overhead and significant speed-up (nearly 10x faster than serial algorithms on 50 nodes).
  • piES shows substantially faster convergence than pLSA across all tested optimization conditions.
  • The piES algorithm scales effectively with an increasing number of nodes.

Conclusions:

  • The piES algorithm is demonstrably faster and more reliable than pLSA for gene regulatory network inference.
  • piES exhibits superior scalability with increasing computational nodes.
  • The piES algorithm is well-suited for hybrid global/local search and hierarchical evolutionary algorithms, leveraging multi-core architectures.