Fig. 1. Schematic illustration of Si-C method for inferential structure determination from single-cell Hi-C data.

a Building models of chromosomes by using polymer chains consisting of contiguous, equally sized beads, and assigning the experimentally observed contacts to the pair of chromatin beads containing the corresponding restriction fragment ends. b Defining the total potential energy of a 3D conformation. c Performing a structure optimization by using the steepest gradient descent algorithm from an initial conformation to minimize$E\left(\mathbf{R}\right)$.