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

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,...
Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
Phylogeny01:23

Phylogeny

Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
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...

You might also read

Related Articles

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

Sort by
Same author

Spatial mapping, isolation, and culture of primary human microglia and astrocytes: A systematic review and framework for glial cell-based models.

Journal of neuropathology and experimental neurology·2026
Same author

Eucalyptol Ameliorates Neuroendocrine Stress-Aggravated Rheumatoid Arthritis Through Anti-inflammatory, Antioxidant, and Chondroprotective Mechanisms Associated with NF-κB and MAPK Signaling Pathways.

Cureus·2026
Same author

Reimagining plant science training in the era of generative artificial intelligence: a global perspective.

The Plant cell·2026
Same author

QIM26-290: Harnessing Artificial Intelligence for Quality Improvement: The RESCUE Score - A First-of-Its-Kind AI Framework for Quality Evaluation and Outcome Correlation in Resource-Limited Bone Marrow Transplantation Programs.

Journal of the National Comprehensive Cancer Network : JNCCN·2026
Same author

CD163 Outperforms CD68 in Clear Cell Renal Cell Carcinoma: Clinicopathological and Prognostic Correlations.

Annals of African medicine·2026
Same author

QIM26-290: Harnessing Artificial Intelligence for Quality Improvement: The RESCUE Score - A First-of-Its-Kind AI Framework for Quality Evaluation and Outcome Correlation in Resource-Limited Bone Marrow Transplantation Programs.

Journal of the National Comprehensive Cancer Network : JNCCN·2026
Same journal

Analysis of strength degradation of coal and rock masses and stability of mined areas under long term immersion environment.

PloS one·2026
Same journal

Biogenic Silver-Selenium nanocomposite with anticancer activity and potent efficacy against vancomycin-resistant Staphylococcus aureus.

PloS one·2026
Same journal

Preparation and physicochemical characterization of a biodegradable chitosan/carboxymethyl cellulose hydrogel synthesized in NaOH/urea medium.

PloS one·2026
Same journal

Action-guilt, survivor-guilt, and depression in combat-related PTSD.

PloS one·2026
Same journal

Explainable machine learning for predicting activities of daily living at discharge in stroke patients: A retrospective study using SHAP interpretability.

PloS one·2026
Same journal

Deep learning based two-way feature depiction model for brain tumor detection.

PloS one·2026
See all related articles

Related Experiment Video

Updated: May 19, 2026

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

NEXCADE: perturbation analysis for complex networks.

Gitanjali Yadav1, Suresh Babu

  • 1Computational Biology Laboratory, National Institute of Plant Genome Research, New Delhi, India. gy@nipgr.res.in

Plos One
|August 8, 2012
PubMed
Summary
This summary is machine-generated.

NEXCADE is a new software tool that uses network theory to simulate disturbances in complex systems. It helps identify critical nodes for system robustness and resilience against failures.

More Related Videos

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks
09:49

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks

Published on: September 25, 2021

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

Related Experiment Videos

Last Updated: May 19, 2026

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

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks
09:49

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks

Published on: September 25, 2021

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

Area of Science:

  • Network theory
  • Systems biology
  • Computational ecology

Background:

  • Complex systems exhibit 'robust, yet fragile' properties.
  • Network theory is applied to understand interactions in biology, sociology, and ecology.
  • Simulating system responses to perturbations is crucial for risk assessment.

Purpose of the Study:

  • Develop NEXCADE, an automated and interactive program for simulating network perturbations.
  • Assess changes in global network topology and connectivity under induced disturbances.
  • Provide a tool for identifying critical nodes and devising resilience strategies.

Main Methods:

  • Utilize graph theory to simulate perturbations in user-defined ways (singly, clusters, sequentially).
  • Apply NEXCADE to diverse real-world networks: protein-protein interactions, fungal biochemical networks, ecological food webs, and social networks.
  • Enable step-by-step network visualization and risk assessment.

Main Results:

  • NEXCADE effectively simulates perturbations and visualizes their impact on network topology.
  • The software identifies critical nodes essential for system robustness.
  • Demonstrated utility across various complex systems, highlighting its broad applicability.

Conclusions:

  • NEXCADE offers a powerful approach for analyzing the robustness and fragility of complex systems.
  • The tool facilitates risk assessment and the development of strategies for network resilience.
  • NEXCADE is available as downloadable software and an OS-independent web server for the scientific community.