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

Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

9.0K
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
9.0K
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

3.3K
3.3K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

11.6K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
11.6K
Genomic Imprinting and Inheritance02:30

Genomic Imprinting and Inheritance

36.9K
Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
36.9K
Causality in Epidemiology01:21

Causality in Epidemiology

1.5K
Causality or causation is a fundamental concept in epidemiology, vital for understanding the relationships between various factors and health outcomes. Despite its importance, there's no single, universally accepted definition of causality within the discipline. Drawing from a systematic review, causality in epidemiology encompasses several definitions, including production, necessary and sufficient, sufficient-component, counterfactual, and probabilistic models. Each has its strengths and...
1.5K
Genomics02:02

Genomics

39.9K
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...
39.9K

You might also read

Related Articles

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

Sort by
Same author

T cell development from expanded hematopoietic progenitors reveals initiation control by <i>Lmo2</i> and Flt3L priming.

Science immunology·2026
Same author

Ever-evolving insights into the cellular and molecular drivers of lymphoid cell development.

Experimental hematology·2024
Same author

Transcriptional network dynamics in early T cell development.

The Journal of experimental medicine·2024
Same author

T-cell commitment inheritance-an agent-based multi-scale model.

NPJ systems biology and applications·2024
Same author

A Bcl11b<sup>N797K</sup> variant isolated from an immunodeficient patient inhibits early thymocyte development in mice.

Frontiers in immunology·2024
Same author

Multiplex, Quantitative, High-Resolution Imaging of Protein:Protein Complexes via Hybridization Chain Reaction.

ACS chemical biology·2024

Related Experiment Video

Updated: Jan 25, 2026

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

2.6K

Causal Gene Regulatory Network Modeling and Genomics: Second-Generation Challenges.

Ellen V Rothenberg1

  • 1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|May 8, 2019
PubMed
Summary
This summary is machine-generated.

Gene regulatory network models advance developmental biology. Expanding these models to complex mammalian systems requires addressing challenges like chromatin accessibility, transcription factor dose, and regulatory syntax.

Keywords:
developmental kineticsdevelopmental regulationepigenetic constraintgene silencing and de-repressionmodeling causality

More Related Videos

Generation of Human Chimeric Antigen Receptor Regulatory T Cells
10:29

Generation of Human Chimeric Antigen Receptor Regulatory T Cells

Published on: January 3, 2025

2.4K
Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
07:55

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

10.7K

Related Experiment Videos

Last Updated: Jan 25, 2026

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

2.6K
Generation of Human Chimeric Antigen Receptor Regulatory T Cells
10:29

Generation of Human Chimeric Antigen Receptor Regulatory T Cells

Published on: January 3, 2025

2.4K
Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
07:55

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

10.7K

Area of Science:

  • Developmental Biology
  • Systems Biology
  • Computational Biology

Background:

  • Gene regulatory network (GRN) modeling is crucial for understanding developmental systems.
  • Ordinary differential equation (ODE) and Boolean models have explained subcircuit dynamics.
  • Global GRN models have predicted embryonic body plan development.

Purpose of the Study:

  • To explore the expansion of GRN modeling to post-embryonic mammalian systems.
  • To identify key theoretical challenges for more quantitative and predictive GRN models.

Main Methods:

  • This perspective discusses theoretical problems and challenges.
  • It examines limitations of current modeling approaches (ODE and Boolean).

Main Results:

  • Several critical problems hinder the expansion of GRN models to mammalian systems.
  • These include chromatin state effects, transcription factor dose dependence, transcriptional stochasticity, epigenetic delays, repression types, and multi-enhancer regulatory syntax.

Conclusions:

  • Overcoming these challenges is essential for developing more predictive GRN models for complex developmental systems.
  • Further quantitative and theoretical advancements are needed to apply GRN modeling beyond embryonic development.