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

3D genome reconstruction from chromosomal contacts.

Author information

1
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.
2
Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Université Pierre et Marie Curie, Sorbonne Universités, Paris, France.
3
Institut Pasteur, Group Spatial Regulation of Genomes, Department of Genomes and Genetics, Paris, 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.

PMID:
25240436
DOI:
10.1038/nmeth.3104
[Indexed for MEDLINE]

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