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

4.9K
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...
4.9K
Propagation of Action Potentials01:23

Propagation of Action Potentials

6.4K
The propagation of an action potential refers to the process by which a nerve impulse, or "action potential," travels along a neuron.
Neurons (nerve cells) have a resting membrane potential, with a slightly negative charge inside compared to outside. This is maintained by ion channels, such as sodium (Na+) and potassium (K+) channels, which control the flow of ions. When a stimulus, like a touch or a signal from another neuron, triggers the neuron, sodium channels open, allowing sodium ions to...
6.4K
IP3/DAG Signaling Pathway01:11

IP3/DAG Signaling Pathway

12.3K
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...
12.3K
Protein Networks02:26

Protein Networks

4.0K
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,...
4.0K
Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

6.4K
Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
6.4K
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

59
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...
59

You might also read

Related Articles

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

Sort by
Same author

Diagnostic Performance of [18 F] FDOPA PET/CT and Other Tracers in Pheochromocytoma: A Meta-Analysis.

Academic radiology·2024
Same author

Multiomics integrated analysis and experimental validation identify TLR4 and ALOX5 as oxidative stress-related biomarkers in intracranial aneurysms.

Journal of neuroinflammation·2024
Same author

Asymmetric catalytic concise synthesis of 3-(3-indolomethyl)-oxindoles for the construction of trigolute analogs.

Chemical communications (Cambridge, England)·2024
Same author

Dipole Moment Modulation of Terminal Groups Enables Asymmetric Acceptors Featuring Medium Bandgap for Efficient and Stable Ternary Organic Solar Cells.

Angewandte Chemie (International ed. in English)·2024
Same author

Role of blood lipids in mediating the effect of dietary factors on gastroesophageal reflux disease: a two-step mendelian randomization study.

European journal of nutrition·2024
Same author

Tough polyacrylic acid hydrogels with stable swelling and active functionalities enabled by quaternized cellulose nanofibrils and iron ions for absorbent pad interlayers.

Carbohydrate polymers·2024
Same journal

Trust, Reproducibility, and Progress: The Roles of Independent Blind Prediction and Assessment and Benchmarking in Computational Biology.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

The Evolving Cyberinfrastructure at the National Institutes of Health to Support Data and AI in Biomedical Research.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

Applications of AI & ML in Biomanufacturing of Cell and Gene Therapies.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

AI for Health: Leveraging Artificial Intelligence to Revolutionize Healthcare.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

Workshop Introduction: Advances of AI Methods in Single Cell Spatial Omics.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

DRIVE-KG: Enhancing variant-phenotype association discovery in understudied complex diseases using heterogeneous knowledge graphs.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
See all related articles

Related Experiment Video

Updated: Aug 16, 2025

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

2.2K

Integrated Graph Propagation and Optimization with Biological Applications.

Krithika Krishnan1, Tiange Shi, Han Yu

  • 1Institute of Artificial Intelligence and Data Science, University at Buffalo, Buffalo, NY 14214, USA.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|December 21, 2022
PubMed
Summary
This summary is machine-generated.

This study introduces Integrated Graph Propagation and Optimization (IGPON), a novel method for optimizing biological networks. IGPON identifies optimal perturbation patterns to steer networks toward desired states, bypassing complex dynamic models.

More Related Videos

Author Spotlight: An Optimized Automated Method for Investigating Retinoic Acid Receptors in Neuronal Mitochondria
08:33

Author Spotlight: An Optimized Automated Method for Investigating Retinoic Acid Receptors in Neuronal Mitochondria

Published on: July 28, 2023

665
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

17.8K

Related Experiment Videos

Last Updated: Aug 16, 2025

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

2.2K
Author Spotlight: An Optimized Automated Method for Investigating Retinoic Acid Receptors in Neuronal Mitochondria
08:33

Author Spotlight: An Optimized Automated Method for Investigating Retinoic Acid Receptors in Neuronal Mitochondria

Published on: July 28, 2023

665
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

17.8K

Area of Science:

  • Systems Biology
  • Computational Biology
  • Network Science

Background:

  • Mathematical models are crucial for biological systems analysis.
  • Dynamic models are often limited by complex functional forms and unknown parameters.
  • Network propagation offers a parameter-free approach to assess node sensitivity, approximating Jacobian matrices.

Purpose of the Study:

  • To develop a novel computational framework, Integrated Graph Propagation and Optimization (IGPON).
  • To identify optimal perturbation strategies for biological networks.
  • To drive biological networks towards desired target states efficiently.

Main Methods:

  • Developed IGPON, integrating network propagation into an objective function.
  • Utilized a propagation-based sensitivity matrix as a Jacobian approximation.
  • Employed Broyden's method for optimization.

Main Results:

  • IGPON effectively optimizes both directed and undirected networks.
  • The method demonstrated robustness against uncertainties in network structure.
  • Successful application to simulated, in silico, and biological pathway data.

Conclusions:

  • IGPON provides an effective and robust approach for network optimization in systems biology.
  • The method overcomes limitations of traditional dynamic modeling.
  • Enables precise control of biological networks towards specific functional states.