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Updated: Apr 23, 2026

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
Published on: May 6, 2010
3D genome reconstruction from chromosomal contacts
Annick Lesne1, Julien Riposo2, Paul Roger2
11] 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.
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.
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