Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Epigenetic Regulation

Epigenetic Regulation

Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.

Epigenetic Regulation

Epigenetic Regulation

Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. This regulation ensures that each cell produces only proteins necessary for its function. For example, proteins that promote bone growth are not produced in muscle cells. Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
X-chromosome...

Genome-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

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...

Model Approaches for Pharmacokinetic Data: Distributed Parameter Models

Model Approaches for Pharmacokinetic Data: Distributed Parameter Models

Pharmacokinetic models are mathematical constructs that represent and predict the time course of drug concentrations in the body, providing meaningful pharmacokinetic parameters. These models are categorized into compartment, physiological, and distributed parameter models.
The distributed parameter models are specifically designed to account for variations and differences in some drug classes. This model is particularly useful for assessing regional concentrations of anticancer or...

One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for ka Estimation

One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for k_a Estimation

This lesson introduces two critical methods in pharmacokinetics, the Wagner-Nelson and Loo-Riegelman methods, used for estimating the absorption rate constant (ka) for drugs administered via non-intravenous routes. The Wagner-Nelson method relates ka to the plasma concentration derived from the slope of a semilog percent unabsorbed time plot. However, it is limited to drugs with one-compartment kinetics and can be impacted by factors like gastrointestinal motility or enzymatic degradation.
On...

Mechanistic Models: Compartment Models in Individual and Population Analysis

Mechanistic Models: Compartment Models in Individual and Population Analysis

Mechanistic models are utilized in individual analysis using single-source data, but imperfections arise due to data collection errors, preventing perfect prediction of observed data. The mathematical equation involves known values (Xi), observed concentrations (Ci), measurement errors (εi), model parameters (ϕj), and the related function (ƒi) for i number of values. Different least-squares metrics quantify differences between predicted and observed values. The ordinary least...

You might also read

Related Articles

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

Sort by

Same author

Presence of retinal pericyte-reactive autoantibodies in diabetic retinopathy patients.

Scientific reports·2016

Same author

Computational Analysis of Structure-Based Interactions for Novel H₁-Antihistamines.

International journal of molecular sciences·2016

Same author

Mixed Spectrum Analysis on fMRI Time-Series.

IEEE transactions on medical imaging·2016

Same author

Ultra-Low Power Dynamic Knob in Adaptive Compressed Sensing Towards Biosignal Dynamics.

IEEE transactions on biomedical circuits and systems·2016

Same author

Hepatic Stellate Cells Directly Inhibit B Cells via Programmed Death-Ligand 1.

Journal of immunology (Baltimore, Md. : 1950)·2016

Same author

Use of emergency department imaging in patients with minor trauma.

The Journal of surgical research·2016

Search research articles

Related Experiment Video

Updated: Mar 8, 2026

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

NetLand: quantitative modeling and visualization of Waddington's epigenetic landscape using probabilistic potential.

Jing Guo^1,2, Feng Lin¹, Xiaomeng Zhang¹

¹Biomedical Informatics Lab, School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore.

Bioinformatics (Oxford, England)

|January 22, 2017

Summary

This summary is machine-generated.

NetLand is a new open-source software tool that models gene regulatory networks and visualizes Waddington's epigenetic landscape. It overcomes previous limitations, enabling better understanding of cell fate determination.

More Related Videos

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Published on: March 1, 2024

Pattern-based Search of Epigenomic Data Using GeNemo

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

Related Experiment Videos

Last Updated: Mar 8, 2026

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Published on: March 1, 2024

Pattern-based Search of Epigenomic Data Using GeNemo

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

Area of Science:

Computational biology
Systems biology
Genetics

Background:

Waddington's epigenetic landscape is a key metaphor for cellular dynamics.
Quantitative modeling and visualization of gene regulatory networks (GRNs) are challenging, especially for complex networks.
No dedicated software tool for Waddington's landscape modeling was previously available.

Purpose of the Study:

To introduce NetLand, an open-source software tool for modeling GRNs and visualizing Waddington's epigenetic landscape.
To provide a user-friendly interface for exploring cell fate regulation.
To facilitate knowledge discovery and experimental design in stem cell differentiation and reprogramming.

Main Methods:

NetLand models the kinetic dynamics of gene regulatory networks (GRNs).
It visualizes the corresponding Waddington's epigenetic landscape in three dimensions.
The software supports GRNs with any number of genes and features an interactive graphical user interface.

Main Results:

NetLand enables quantitative modeling and 3D visualization of Waddington's epigenetic landscape for GRNs of any size.
The software provides an accessible platform for simulating cellular dynamics.
It facilitates the study of complex biological processes like cell fate determination.

Conclusions:

NetLand addresses the need for a software tool to model and visualize Waddington's epigenetic landscape for complex GRNs.
The tool's interactive interface supports knowledge discovery and experimental design in cell fate regulation.
NetLand is an open-source solution available for Windows, Linux, and OS X.