GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data

Oluwatosin Oluwadare, Max Highsmith, Douglass Turner, Erez Lieberman-Aiden, Jianlin Cheng

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12 Citations (Web of Science)


Advances in the study of chromosome conformation capture technologies, such as Hi-C technique - capable of capturing chromosomal interactions in a genome-wide scale - have led to the development of three-dimensional chromosome and genome structure reconstruction methods from Hi-C data. The three dimensional genome structure is important because it plays a role in a variety of important biological activities such as DNA replication, gene regulation, genome interaction, and gene expression. In recent years, numerous Hi-C datasets have been generated, and likewise, a number of genome structure construction algorithms have been developed. In this work, we outline the construction of a novel Genome Structure Database (GSDB) to create a comprehensive repository that contains 3D structures for Hi-C datasets constructed by a variety of 3D structure reconstruction tools. The GSDB contains over 50,000 structures from 12 state-of-the-art Hi-C data structure prediction algorithms for 32 Hi-C datasets. GSDB functions as a centralized collection of genome structures which will enable the exploration of the dynamic architectures of chromosomes and genomes for biomedical research. GSDB is accessible at

Original languageEnglish
Article number60
JournalBMC Molecular and Cell Biology
Issue number1
Publication statusPublished - 5 Aug 2020
Externally publishedYes


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