title: Modeling chromosomes: Beyond pretty pictures.
abstract: Recently, Chromosome Conformation Capture (3C) based experiments have highlighted the importance of computational models for the study of chromosome organization. In this review, we propose that current computational models can be grouped into roughly four classes, with two classes of data-driven models: consensus structures and data-driven ensembles, and two classes of de novo models: structural ensembles and mechanistic ensembles. Finally, we highlight specific questions mechanistic ensembles can address.
authors.affiliation: Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Maxim V
authors.initials: MV
authors.lastname: Imakaev
authors.affiliation: Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Geoffrey
authors.initials: G
authors.lastname: Fudenberg
authors.affiliation: Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Leonid A
authors.initials: LA
authors.lastname: Mirny
mesh_terms: D000818:Animals; D002843:Chromatin / Q000502:physiology / Q000648:ultrastructure*; D002874:Chromosome Mapping; D003198:Computer Simulation; D006801:Humans; D008958:Models, Molecular
chemical_list: D002843:Chromatin
keywords: Chromatin; Hi-C; Model; Polymer; Simulation