3D genome reconstruction from chromosomal contacts

Nat Methods. 2014 Nov;11(11):1141-3. doi: 10.1038/nmeth.3104. Epub 2014 Sep 21.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Chromosomes, Fungal*
  • Chromosomes, Human*
  • Computer Simulation*
  • Genome, Fungal*
  • Genome, Human*
  • Humans
  • Imaging, Three-Dimensional / methods*
  • Nucleic Acid Conformation
  • Software
  • Yeasts / genetics*