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Protein Networks02:26

Protein Networks

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,...
Protein Networks02:26

Protein Networks

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,...
Sequence Networks of Rotating Machines01:24

Sequence Networks of Rotating Machines

A Y-connected synchronous generator, grounded through a neutral impedance, is designed to produce balanced internal phase voltages with only positive-sequence components. The generator's sequence networks include a source voltage that is exclusively in the positive-sequence network. The sequence components of line-to-ground voltages at the generator terminals illustrate this configuration.
Zero-sequence current induces a voltage drop across the generator's neutral impedance and other...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Synthetic Biology02:55

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
Genetic Screens02:46

Genetic Screens

Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...

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Related Experiment Video

Updated: May 7, 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

A pattern-oriented specification of gene network inference processes.

Nestor W Trepode1, Cléver R G de Farias, Junior Barrera

  • 1Department of Computer Science and Mathematics (DCM), Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Av. Bandeirantes, 3900, Monte Alegre, Ribeirão Preto 14040-901, SP, Brazil.

Computers in Biology and Medicine
|September 17, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces a pattern-oriented specification for inferring genetic regulatory networks. The approach integrates microarray data and biological knowledge, offering a structured solution for gene network analysis.

Keywords:
Dynamical system identificationGene network inferenceGenetic regulatory networksMicroarray data analysisPatternsProcess modeling

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Last Updated: May 7, 2026

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

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Patterns are established in Computer Science for reusable solutions.
  • Process specifications benefit from pattern-oriented approaches for clarity.
  • Genetic regulatory network inference is crucial for understanding cellular mechanisms.

Purpose of the Study:

  • To present a pattern-oriented specification for genetic regulatory network inference.
  • To integrate microarray data and prior biological knowledge within this framework.
  • To evaluate the specification against current trends in gene network inference.

Main Methods:

  • Developed a pattern-oriented specification for the gene inference process.
  • Utilized microarray data as input.
  • Incorporated prior biological knowledge into the model.
  • Evaluated the specification against existing literature.

Main Results:

  • A novel pattern-oriented specification for genetic regulatory network inference was proposed.
  • The specification effectively integrates diverse data types.
  • The approach aligns with contemporary gene network inference methodologies.

Conclusions:

  • Pattern-oriented specifications offer a robust framework for complex biological processes like gene network inference.
  • The proposed method provides a structured and adaptable solution for analyzing gene expression data.
  • This work contributes to advancing the field of computational systems biology.