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

Three-Dimensional Microscopy in Microbiology01:28

Three-Dimensional Microscopy in Microbiology

740
Three-dimensional imaging techniques are essential in cell biology, allowing researchers to visualize intricate cellular structures with high resolution. Two prominent methods, Differential Interference Contrast Microscopy (DIC) and Confocal Scanning Laser Microscopy (CSLM), provide distinct advantages for imaging live and thick specimens, respectively.Differential Interference Contrast MicroscopyDIC microscopy enhances contrast in transparent, unstained samples by converting phase...
740
Molecular Models02:00

Molecular Models

43.4K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
43.4K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

20.5K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
20.5K
Genomics02:02

Genomics

39.5K
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...
39.5K

You might also read

Related Articles

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

Sort by
Same author

Zebrafish knock-in lines enabling live visualization of extracellular matrix dynamics during development and regeneration.

Development (Cambridge, England)·2026
Same author

Enhancer-directed gene delivery for digit regeneration based on conserved epidermal factors.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Enhancer-directed gene delivery for digit regeneration based on conserved epidermal factors.

bioRxiv : the preprint server for biology·2026
Same author

The hard truth about how hard it is to publish in Development.

Development (Cambridge, England)·2026
Same author

Epicardial Tcf21 facilitates cardiomyocyte dedifferentiation and heart regeneration in zebrafish.

Developmental biology·2025
Same author

Live visualization of extracellular matrix dynamics during development and regeneration in zebrafish.

bioRxiv : the preprint server for biology·2025

Related Experiment Video

Updated: Jan 8, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.0K

geomeTriD: a Bioconductor package for interactive and integrative visualization of 3D structural model with

Jianhong Ou1, Kenneth D Poss1,2

  • 1Morgridge Institute for Research, Madison, WI 53715, United States.

Bioinformatics Advances
|December 16, 2025
PubMed
Summary

GeomeTriD is a new R package for visualizing and comparing 3D genome structures. It enables interactive exploration of chromatin organization and aids in understanding gene regulation across different conditions.

More Related Videos

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

411.3K
Mapping Mammalian 3D Genome Interactions with Micro-C-XL
11:41

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

3.5K

Related Experiment Videos

Last Updated: Jan 8, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.0K
Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

411.3K
Mapping Mammalian 3D Genome Interactions with Micro-C-XL
11:41

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

3.5K

Area of Science:

  • Genomics
  • Computational Biology
  • Bioinformatics

Background:

  • The three-dimensional genome organization is crucial for gene expression regulation.
  • High-throughput chromosome conformation capture (Hi-C) and other methods map chromatin dynamics.
  • Comparing and integrating multi-layer genomic annotations of chromatin structure is challenging.

Purpose of the Study:

  • To develop a flexible R-integrated framework for interactive 3D genome visualization and comparison.
  • To address limitations in existing tools for exploring chromatin structures across conditions and with custom annotations.

Main Methods:

  • Developed geomeTriD, an R/Bioconductor package.
  • Utilized three.js for interactive 3D chromatin structure visualization.
  • Integrated multi-layer annotation capabilities and side-by-side comparison of chromatin states.
  • Ensured compatibility with Shiny-based analysis workflows.

Main Results:

  • GeomeTriD provides interactive visualization of chromatin structures.
  • The package supports multi-layer genomic annotation.
  • It allows parallel comparison of two distinct chromatin states.
  • GeomeTriD is compatible with Shiny applications for advanced analysis.

Conclusions:

  • GeomeTriD facilitates the reconstruction and comparison of 3D genome structures.
  • It links chromatin architecture to gene regulation, epigenetic states, and cell-state transitions.
  • The package will aid researchers in analyzing complex multi-omic and spatial genomic datasets.