title: 3D genome reconstruction from chromosomal contacts.
abstract: A computational challenge raised by chromosome conformation capture (3C) experiments is to reconstruct spatial distances and three-dimensional genome structures from observed contacts between genomic loci. We propose a two-step algorithm, ShRec3D, and assess its accuracy using both in silico data and human genome-wide 3C (Hi-C) data. This algorithm avoids convergence issues, accommodates sparse and noisy contact maps, and is orders of magnitude faster than existing methods.
authors.affiliation: 1] Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Université Pierre et Marie Curie, Sorbonne Universités, Paris, France. [2] Institut de Génétique Moléculaire de Montpellier, CNRS UMR 5535, Université de Montpellier, Montpellier, France.
authors.forename: Annick
authors.initials: A
authors.lastname: Lesne
authors.affiliation: Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Université Pierre et Marie Curie, Sorbonne Universités, Paris, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Riposo
authors.affiliation: Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Université Pierre et Marie Curie, Sorbonne Universités, Paris, France.
authors.forename: Paul
authors.initials: P
authors.lastname: Roger
authors.affiliation: Institut Pasteur, Group Spatial Regulation of Genomes, Department of Genomes and Genetics, Paris, France.
authors.forename: Axel
authors.initials: A
authors.lastname: Cournac
authors.affiliation: Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Université Pierre et Marie Curie, Sorbonne Universités, Paris, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Mozziconacci
mesh_terms: D000465:Algorithms; D015825:Chromosomes, Fungal; D002877:Chromosomes, Human; D003198:Computer Simulation; D016681:Genome, Fungal; D015894:Genome, Human; D006801:Humans; D021621:Imaging, Three-Dimensional / Q000379:methods*; D009690:Nucleic Acid Conformation; D012984:Software; D015003:Yeasts / Q000235:genetics*