Schematic overview of the 3D-GNOME pipeline. (A) Processed ChIA-PET library sequencing reads including the enriched PET clusters and the nonenriched PET singletons are the data sets to be used for 3D modeling. (B) PET reads are aggregated to construct 2D contact heat maps for each chromosome. Heat maps can be optionally de-noised using a graph distance (GD) normalization approach. (C) A model of a single chromosome (Chromosome 10) at low (left) and high (right) resolutions. (D) Whole-genome model at three different scales for GM12878 cells. (E) Structures are analyzed using a fully interactive 3D viewer. Genomic annotations may be overlaid on the structure to facilitate analysis. The marks depicted here were obtained from the ENCODE Project.