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

Synthetic Biology02:55

Synthetic Biology

4.7K
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...
4.7K
Genomics02:02

Genomics

35.6K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
35.6K
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

12.3K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
12.3K
The Roles of Bacteria and Fungi in Plant Nutrition02:11

The Roles of Bacteria and Fungi in Plant Nutrition

34.9K
Plants have the impressive ability to create their own food through photosynthesis. However, plants often require assistance from organisms in the soil to acquire the nutrients they need to function correctly. Both bacteria and fungi have evolved symbiotic relationships with plants that help the species to thrive in a wide variety of environments.
34.9K
Steps in Outbreak Investigation01:18

Steps in Outbreak Investigation

102
In the ever-evolving field of public health, statistical analysis serves as a cornerstone for understanding and managing disease outbreaks. By leveraging various statistical tools, health professionals can predict potential outbreaks, analyze ongoing situations, and devise effective responses to mitigate impact. For that to happen, there are a few possible stages of the analysis:
102

You might also read

Related Articles

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

Sort by
Same author

The impact of western versus agrarian diet consumption on gut microbiome composition and immune dysfunction in people living with HIV in rural and urban Zimbabwe.

Microbiome·2026
Same author

Dynamic thermodynamic-informational entropic relationship (TIER) models of selective vulnerability to neurodegeneration.

bioRxiv : the preprint server for biology·2026
Same author

Amoxicillin induces gut dysbiosis leading to long term suppression of type-17 immune tone in the lungs.

bioRxiv : the preprint server for biology·2026
Same author

Desiderata for a biomedical knowledge network: opportunities, challenges and future directions.

Bioinformatics advances·2026
Same author

Governing real-world health data as a public utility.

Science (New York, N.Y.)·2026
Same author

Gut microbiome composition influences immunologic alterations in the blood and gut of HIV-positive and HIV-negative men who have sex with men.

Frontiers in immunology·2026
Same journal

Turbulent flow in a vortex separator with a directed pipe inlet.

Scientific reports·2026
Same journal

Systematic characteristic evaluation of clay-based cementitious material derived from calcium carbide residue and waste tile powder.

Scientific reports·2026
Same journal

Retraction Note: Improvement of a rapid diagnostic application of monoclonal antibodies against avian influenza H7 subtype virus using Europium nanoparticles.

Scientific reports·2026
Same journal

Applying large language models to spam detection in the Kazakh low-resource language setting.

Scientific reports·2026
Same journal

An open-source 3D printing system enabling in-situ freeze-thaw processing of hydrogels.

Scientific reports·2026
Same journal

An enhanced EfficientNet framework for automated waste classification using cosine annealing and label smoothing.

Scientific reports·2026
See all related articles

Related Experiment Video

Updated: May 25, 2025

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports
07:35

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

Published on: October 13, 2023

1.5K

Hypothesizing mechanistic links between microbes and disease using knowledge graphs.

Brook E Santangelo1, Michael Bada2, Lawrence E Hunter2

  • 1Department of Biomedical Informatics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA. brook.santangelo@cuanschutz.edu.

Scientific Reports
|February 26, 2025
PubMed
Summary
This summary is machine-generated.

Knowledge graphs can now generate mechanistic hypotheses for gut microbiome and disease links. This approach, using MGMLink, aids in understanding host-microbe interactions for conditions like inflammatory bowel disease and Parkinson's disease.

Keywords:
Computational biologyEmbedding methodsKnowledge graphsMicrobiome

More Related Videos

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease
09:52

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

Published on: January 10, 2025

471
Kinetic Visualization of Single-Cell Interspecies Bacterial Interactions
08:33

Kinetic Visualization of Single-Cell Interspecies Bacterial Interactions

Published on: August 5, 2020

6.8K

Related Experiment Videos

Last Updated: May 25, 2025

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports
07:35

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

Published on: October 13, 2023

1.5K
A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease
09:52

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

Published on: January 10, 2025

471
Kinetic Visualization of Single-Cell Interspecies Bacterial Interactions
08:33

Kinetic Visualization of Single-Cell Interspecies Bacterial Interactions

Published on: August 5, 2020

6.8K

Area of Science:

  • Biomedical informatics
  • Microbiome research
  • Systems biology

Background:

  • Gut microbiome alterations correlate with various diseases.
  • Mechanistic understanding of host-microbe interactions in disease is challenging.
  • Knowledge graphs effectively represent complex biological concepts.

Purpose of the Study:

  • To demonstrate the potential of knowledge graphs for hypothesizing mechanistic explanations of host-microbe interactions in disease.
  • To develop a scalable and comprehensive approach for generating these hypotheses.

Main Methods:

  • Construction of a knowledge graph (MGMLink) linking microbes, genes, and metabolites.
  • Utilizing shortest path or template-based searches within the knowledge graph.
  • Application of a novel path-prioritization methodology for hypothesis inference.

Main Results:

  • The developed methodology supports the inference of mechanistic hypotheses for observed microbe-disease phenotype relationships.
  • Demonstrated applications in inflammatory bowel disease and Parkinson's disease.
  • The approach enables scalable and comprehensive generation of mechanistic hypotheses.

Conclusions:

  • Knowledge graphs, specifically MGMLink, offer a powerful tool for elucidating mechanistic links between the gut microbiome and disease.
  • This methodology facilitates a deeper understanding of complex host-microbe interactions.
  • The approach has significant implications for biomedical research and disease mechanism discovery.