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

Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

86
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
86
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

61
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
61
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.1K
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...
6.1K
Microbial Classification System01:24

Microbial Classification System

138
Classification is the process of organizing organisms into hierarchically inclusive groups based on their phenotypic similarities or evolutionary relationships. A species comprises one or more strains, and closely related species are grouped into genera. Genera are further classified into families, families into orders, orders into classes, and so forth, up to the domain level, which is the broadest taxonomic rank derived from a combination of phenotypic and genotypic data.The nomenclature of...
138
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

12.7K
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
12.7K
The Tree of Life - Bacteria, Archaea, Eukaryotes02:40

The Tree of Life - Bacteria, Archaea, Eukaryotes

32.9K
The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both...
32.9K

You might also read

Related Articles

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

Sort by
Same author

A Unified Bayesian Framework for Cross-Technology Collision Cross Section Postcalibration Correction and Multilaboratory Harmonization.

Analytical chemistry·2026
Same author

Linking Climate Features to Human Life Expectancy in the United States: Implications for Integrated Climate and Health Policies.

The journal of climate change and health·2026
Same author

tDCS improves early Alzheimer's disease by synaptic vesicle fusion and release.

Military Medical Research·2026
Same author

Computational framework for therapeutic target discovery via perturbation simulation: application to cystic fibrosis airway disease.

Briefings in bioinformatics·2026
Same author

Impact of non-standardized reporting on reproducibility, usability, and integration in nasopharyngeal metagenomic research: a systematic review.

Frontiers in microbiology·2026
Same author

Organophosphate Flame Retardants Disrupt Autism-Relevant Gene Networks Across Development: A Cross-Species Multi-Omics Study.

Environmental research·2025
Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026
Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026
Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026
Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026
Same journal

Dual channel drug-drug interactions extraction based on cross attention.

BMC bioinformatics·2026
Same journal

FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins.

BMC bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Aug 22, 2025

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

4.4K

C3NA: correlation and consensus-based cross-taxonomy network analysis for compositional microbial data.

Kuncheng Song1, Yi-Hui Zhou2

  • 1Bioinformatics Research Center, Biological Sciences, North Carolina State University, Raleigh, NC, USA.

BMC Bioinformatics
|November 8, 2022
PubMed
Summary
This summary is machine-generated.

This study introduces Correlation and Consensus-based Cross-taxonomy Network Analysis (C3NA), an R package for microbial co-occurrence network analysis. C3NA helps identify disease-related microbial taxa relationships and functional patterns.

Keywords:
Co-occurrence network analysisConsensus clusteringMicrobiomeModule preservation analysisR package

More Related Videos

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
09:29

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Published on: May 15, 2019

19.6K
A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

178

Related Experiment Videos

Last Updated: Aug 22, 2025

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

4.4K
Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
09:29

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Published on: May 15, 2019

19.6K
A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

178

Area of Science:

  • Microbiology
  • Bioinformatics
  • Computational Biology

Background:

  • Microbial co-occurrence network structure is crucial for understanding host-microbe-disease relationships.
  • Tools are needed to analyze these networks, identify disease-related taxa, and interpret functional relationships.
  • Phylogenetic relationships are important for resolving conflicting functional data in microbial studies.

Purpose of the Study:

  • To develop a user-friendly R package for analyzing microbial sequencing data.
  • To identify and compare co-occurrence patterns across taxonomic levels.
  • To facilitate the investigation of disease-related microbial taxa and their relationships.

Main Methods:

  • Developed Correlation and Consensus-based Cross-taxonomy Network Analysis (C3NA) R package.
  • Implemented interactive graphic user interfaces (Shiny applications) for data analysis.
  • Applied C3NA to analyze microbial data from colorectal cancer and Crohn's disease.

Main Results:

  • C3NA enables the identification and comparison of microbial co-occurrence patterns.
  • Discovered disease-dependent taxa clusters in colorectal cancer and Crohn's disease.
  • Identified overlaps between discovered taxa clusters and known functional taxa from other studies.

Conclusions:

  • C3NA provides a novel pipeline for microbial co-occurrence network analysis.
  • The package enhances taxa-taxa network analysis with refined and enriched insights.
  • Integrated Shiny applications improve usability for interactive data investigation.