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Updated: Feb 4, 2026

Mapping Mammalian 3D Genome Interactions with Micro-C-XL
Published on: November 3, 2023
The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin
Yanli Wang1, Fan Song1, Bo Zhang1
1Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, 16802, USA.
The 3D Genome Browser offers a new way to explore chromatin interactions using an efficient data format. It helps link regulatory elements to target genes and integrates diverse omics data for a complete 3D genome view.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Understanding the 3D genome structure is crucial for deciphering gene regulation.
- Visualizing and analyzing large-scale chromatin interaction data presents significant computational challenges.
Purpose of the Study:
- To introduce the 3D Genome Browser for exploring chromatin interaction data.
- To present a novel, efficient binary data format for Hi-C data.
- To facilitate the integration of diverse omics data with 3D genome structure.
Main Methods:
- Development of the 3D Genome Browser web platform (http://3dgenome.org).
- Design and implementation of a new binary data format for Hi-C data, significantly reducing file size.
- Development of methods for linking distal cis-regulatory elements to target genes.
- Integration capabilities for thousands of additional omics datasets.
Main Results:
- The new data format enables visualization of chromatin interactions over millions of base pairs within seconds.
- The browser supports exploration of over 300 public chromatin interaction datasets and user-uploaded data.
- Multiple functionalities are provided for identifying regulatory element-gene connections.
Conclusions:
- The 3D Genome Browser provides a powerful and efficient platform for 3D genome analysis.
- The novel data format enhances the speed and accessibility of Hi-C data visualization.
- Seamless integration of omics data offers a comprehensive approach to studying genome regulation and structure.
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