Software tools

The goal of the GSDB is to create a comprehensive and common respository that contains 3D structures for Hi-C data from novel 3D structure prediction tools developed over the years. As a major contribution towards this goal, the members of the BDM Lab have published several research papers and made available several chromosome/genome 3D structure modeling tools to the research community. They are listed below.


  • Oluwadare O, Zhang Y, Cheng J. A maximum likelihood algorithm for reconstructing 3D structures of human chromosomes from chromosomal contact data. BMC genomics. 2018 Dec;19(1):161. [at BMC Genomics]
  • T. Trieu, J. Cheng. 3D Genome Structure Modeling by Lorentzian Objective Function. Nucleic Acids Research, accepted, 2016. [at NAR]
  • B. Adhikari, T. Tuan, J. Cheng. Chromosome3D: Reconstructing Three-Dimensional Chromosomal Structures from Hi-C Interaction Frequency Data using Distance Geometry Simulated Annealing. BMC Genomics, 17:886, 2016. [at BMC Genomics]
  • J. Nowotny, A. Wells, O. Oluwadare, L. Xu, R. Cao, T. Trieu, C. He, J. Cheng. GMOL: an interactive tool for 3D genome structure visualization. Scientific Reports, accepted, 2016. [at Scientific Reports]
  • J. Nowotny, S. Ahmed, L. Xu, O. Oluwadare, H. Chen, N. Hensley, T. Trieu, R. Cao, J. Cheng. Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data. BMC Bioinformatics, 16(1):338, 2015.[ at BMC Bioinformatics]
  • T. Tuan, J. Cheng. MOGEN: a tool for reconstructing 3D models of genomes from chromosomal conformation capturing data. Bioinformatics, accepted, 2015. doi: 10.1093/bioinformatics/btv754. [at BMC Bioinformatics]
  • T. Trieu, J. Cheng. Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data. Nucleic Acids Research. 42(7):e52, 2014 [at NAR]
  • Trieu T, Oluwadare O, Cheng J. Hierarchical Reconstruction of High-Resolution 3D Models of Large Chromosomes. Scientific reports. 2019 Mar 21;9(1):4971. [at Scientific Reports]
  • Trieu T, Oluwadare O, Wopata J, Cheng J. GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure. Bioinformatics. 2018 Sep 12. [at Bioinformatics]