3D genome reconstruction from chromosomal contacts

被引：5

作者：

Lesne, Annick ^{[1
,2
]}

Riposo, Julien ^{[1
]}

Roger, Paul ^{[1
]}

Cournac, Axel ^{[3
]}

Mozziconacci, Julien ^{[1
]}

机构：

[1] Univ Paris 06, Sorbonne Univ, Lab Phys Theor Matiere Condensee, CNRS UMR 7600, Paris, France

[2] Univ Montpellier, CNRS UMR 5535, Inst Genet Mol Montpellier, F-34059 Montpellier, France

[3] Inst Pasteur, Grp Spatial Regulat Genomes, Dept Genomes & Genet, Paris, France

来源：

NATURE METHODS | 2014年 / 11卷 / 11期

关键词：

CHROMATIN INTERACTIONS; INTERACTION FREQUENCY; REVEALS; CONFORMATION;

D O I：

10.1038/NMETH.3104

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：1141 / 1143

页数：3

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