Journal
NATURE METHODS
Volume 11, Issue 11, Pages 1141-1143Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/NMETH.3104
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Funding
- UPMC (Universite Pierre et Marie Curie, Sorbonne-Universites) [CONVERGENCE2011, CVG1110]
- French National Cancer Institute [INCa_5960]
- French National Research Agency (ANR) [ANR-13-BSV5-0010-03, ANR-09-PIRI-0024]
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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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