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

IP3/DAG Signaling Pathway01:11

IP3/DAG Signaling Pathway

12.7K
Membrane lipids such as phosphatidylinositol (PI) are precursors for several membrane-bound and soluble second messengers. Specific kinases phosphorylate PI and produce phosphorylated inositol phospholipids. One such inositol phospholipids are the  phosphatidylinositol-4,5 bisphosphate [PI(4,5)P2], present in the inner half of the lipid bilayer. Upon ligand binding, GPCR stimulates Gq proteins to turn on phospholipase Cꞵ. Activated phospholipase Cꞵ cleaves PI(4,5)P2 and...
12.7K
C4 Pathway and CAM01:27

C4 Pathway and CAM

46.6K
Most plants use the C3 pathway for carbon fixation. However, some plants, such as sugar cane, corn, and cacti that grow in hot conditions, use alternative pathways to fix carbon and conserve energy loss due to photorespiration. Photorespiration is the process that occurs when the oxygen concentration is high. Under such conditions, the rubisco enzyme in the Calvin cycle binds O2 instead of CO2, which halts photosynthesis and consumes energy.
C4 Pathway
The C4 pathway is used by plants such as...
46.6K
Synthetic Biology02:55

Synthetic Biology

5.0K
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...
5.0K
cAMP-dependent Protein Kinase Pathways01:25

cAMP-dependent Protein Kinase Pathways

6.9K
Cyclic Adenosine Monophosphate (cAMP) is an essential second messenger that activates protein kinase A (PKA) and regulates various biological processes. A single epinephrine molecule binds to GPCR and activates several heterotrimeric G proteins, each stimulating multiple adenylyl cyclase, amplifying the signal, and synthesizing large numbers of cAMP molecules. Small changes in cAMP concentration affect PKA activity. The binding of four cAMP molecules induces a conformational change in PKA,...
6.9K
Direct Motor Pathways01:11

Direct Motor Pathways

2.8K
The direct motor pathways, also known as the pyramidal tracts, are a group of neural pathways that originate in the brain and descend through the spinal cord. They control the voluntary movement of the body. There are two major direct motor pathways: the corticospinal and the corticobulbar tracts.
The corticospinal tract is responsible for the voluntary movement of the limbs and trunk. It originates in the cerebral cortex of the brain and descends through the cerebrum's internal capsule and...
2.8K
Primary Active Transport01:29

Primary Active Transport

11.7K
In contrast to passive transport, active transport involves a substance being moved through membranes in a direction against its concentration or electrochemical gradient. There are two types of active transport: primary active transport and secondary active transport. Primary active transport utilizes chemical energy from ATP to drive protein pumps embedded in the cell membrane. With energy from ATP, the pumps transport ions against their electrochemical gradients—a direction they would...
11.7K

You might also read

Related Articles

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

Sort by
Same author

Metabolomic Signatures of Relapse and Survival in AML Patients Receiving Allogeneic Hematopoietic Stem Cell Transplantation.

Hematology reports·2026
Same author

TRPM4 Expression as a Predictive Biomarker and a Mechanistic Driver of Acetalax Activity in Prostate Cancer: Preclinical Efficacy Studies.

Molecular cancer therapeutics·2026
Same author

Polypharmacology is an enduring and nearly universal property of kinase inhibitors.

bioRxiv : the preprint server for biology·2026
Same author

The 2025 Westlake Autumn Symposium for Al Proteomics and Virtual Cell.

Genomics, proteomics & bioinformatics·2026
Same author

FLASH-MM: fast and scalable single-cell differential expression analysis using linear mixed-effects models.

Nature communications·2026
Same author

Tutorial: annotation of animal genomes.

Nature protocols·2026
Same journal

Arrayed single-gene perturbations identify drivers of human anterior neural tube closure.

eLife·2026
Same journal

Pervasive relaxed selection on spermatogenesis genes coincident with the evolution of polygyny in gorillas.

eLife·2026
Same journal

Impacts of DNA methylation on H2A.Z deposition and nucleosome stability.

eLife·2026
Same journal

Continuous developmental changes in word recognition and language learning across early childhood.

eLife·2026
Same journal

Multiple event segmentation mechanisms in the human brain.

eLife·2026
Same journal

Optimised genome editing for precise DNA insertion and substitution using prime editors in zebrafish.

eLife·2026
See all related articles

Related Experiment Video

Updated: Oct 11, 2025

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

17.9K

Author-sourced capture of pathway knowledge in computable form using Biofactoid.

Jeffrey V Wong1, Max Franz1, Metin Can Siper2

  • 1The Donnelly Centre, University of Toronto, Toronto, Canada.

Elife
|December 3, 2021
PubMed
Summary
This summary is machine-generated.

Scientists can now make complex biological data machine-readable using Biofactoid. This platform facilitates the integration of gene, protein, and chemical interaction networks for enhanced data analysis and discovery.

Keywords:
computational biologycrowdsourcecuration toolgeneticsgenomicsknowledge basenonepathway analysisscience forumsystems biology

More Related Videos

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

1.8K
Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
05:47

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems

Published on: June 13, 2025

703

Related Experiment Videos

Last Updated: Oct 11, 2025

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

17.9K
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

1.8K
Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
05:47

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems

Published on: June 13, 2025

703

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Scientific literature contains vast amounts of knowledge on gene, protein, and chemical interactions.
  • Extracting and utilizing this knowledge computationally is challenging due to its unstructured format.
  • Integrating diverse biological knowledge sources is crucial for comprehensive data analysis and interpretation.

Purpose of the Study:

  • To introduce Biofactoid, a web-based platform for representing biological interaction networks.
  • To enable the translation of biological knowledge into a machine-readable and computable format.
  • To facilitate computational analysis, search, and discovery of biological interactions.

Main Methods:

  • Development of a web-based platform (Biofactoid) for user input of interaction data.
  • Implementation of a system to translate specified networks into a computable representation.
  • Conducting a pilot study to assess platform usability and encourage scientific adoption.

Main Results:

  • Biofactoid successfully translates user-defined networks of genes, products, and chemical compounds into a computable format.
  • The platform supports the creation of structured biological knowledge bases.
  • A pilot study demonstrated the potential for Biofactoid adoption within the scientific community.

Conclusions:

  • Biofactoid provides a valuable tool for making biological knowledge machine-readable.
  • The platform enhances the integration of diverse biological data for research.
  • Facilitating computational analysis and discovery of biological interactions is a key outcome.