title: 3D Genome Reconstruction with ShRec3D+ and Hi-C Data.
abstract: Hi-C technology, a chromosome conformation capture (3C) based method, has been developed to capture genome-wide interactions at a given resolution. The next challenge is to reconstruct 3D structure of genome from the 3C-derived data computationally. Several existing methods have been proposed to obtain a consensus structure or ensemble structures. These methods can be categorized as probabilistic models or restraint-based models. In this paper, we propose a method, named ShRec3D+, to infer a consensus 3D structure of a genome from Hi-C data. The method is a two-step algorithm which is based on ChromSDE and ShRec3D methods. First, correct the conversion factor by golden section search for converting interaction frequency data to a distance weighted graph. Second, apply shortest-path algorithm and multi-dimensional scaling (MDS) algorithm to compute the 3D coordinates of a set of genomic loci from the distance graph. We validate ShRec3D+ accuracy on both simulation data and publicly Hi-C data. Our test results indicate that our method successfully corrects the parameter with a given resolution, is more accurate than ShRec3D, and is more efficient and robust than ChromSDE.
authors.forename: Jiangeng
authors.initials: J
authors.lastname: Li
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.forename: Xiaodan
authors.initials: X
authors.lastname: Li
mesh_terms: D000465:Algorithms; D000818:Animals; D002875:Chromosomes / Q000737:chemistry / Q000235:genetics; D003198:Computer Simulation; D030541:Databases, Genetic; D005163:Factor Analysis, Statistical; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D007091:Image Processing, Computer-Assisted; D051379:Mice; D009690:Nucleic Acid Conformation