Abstract
The 3D Genome Browser 2.0 (https://3dgenome.fsm.northwestern.edu) is a significantly enhanced online platform designed for the exploration and analysis of 3D genome architecture data, with easy integration with other omics data such as ChIP-seq and ATAC-seq. This major update introduces a completely redesigned user interface (UI) and the addition of many novel analytical features, empowering researchers to effectively explore the extensive collection of the hosted 3D genome datasets and analyze their own data on a local computer. The browser includes an expanded and manually curated data repository, which now incorporates over 700 bulk and single-cell 3D genome datasets, with key annotations such as compartment, topologically associating domains, and loops. We also added a novel structural variation analysis module, which allows users to visualize and reconstruct chromatin contacts maps in the context of genomic rearrangements and facilitate the detection of enhancer-hijacking events. We rebuilt the platform's architecture from the ground up, resulting in substantial performance gains. The modern and intuitive UI ensures that these powerful analytical tools are accessible and easy to navigate, facilitating a streamlined and efficient workflow for users from diverse research backgrounds. The 3D Genome Browser 2.0 serves as a central, open-access resource poised to accelerate discoveries in the field of genomics.