Before revision:  We apply this method to several data sets generated from experiments using the Hi-C or GAM techniques. To illustrate potential applications of our method , we show how the reconstructed couplings can be used to investigate the URLanizationby Brownian Dynamics .
After revision:  We apply this method to several data sets generated from experiments using the Hi-C and GAM experiments rather than estimates of average distances between genomic loci. Specifically, we model the chromosome as a Gaussian polymer with harmonic interactions and extract the coupling coefficients best reproducing the experimental contact probabilities. In contrast to existing methods, we give an exact expression of the contact probabilities at thermodynamic equilibrium. The Gaussian effective model (GEM) reconstructed with our method reproduces experimental contacts with high accuracy. We also show how Brownian Dynamics simulations of our reconstructed GEM can be used to investigate the URLanizationby Brownian Dynamics .