How DNA is organized in three dimensions inside the cell nucleus and how this affects the ways in which cells access, read and interpret genetic information are among the longest standing questions in cell biology. Using newly developed molecular, genomic and computational approaches based on the chromosome conformation capture technology (such as 3C, 4C, 5C and Hi-C), the spatial organization of genomes is being explored at unprecedented resolution. Interpreting the increasingly large chromatin interaction data sets is now posing novel challenges. Here we describe several types of statistical and computational approaches that have recently been developed to analyse chromatin interaction data.National Institutes of Health (U.S.)National Human Genome Research Institute (U.S.) (HG003143)National Human Genome Research Institute (U.S.) (HG003143-06S1)W. M. Keck FoundationSpain. Ministerio de Ciencia e Innovación (BFU2010-19310/BMC)Human Frontier Science Program (Strasbourg, France) (RGP0044/2011)European Union (BLUEPRINT project (EU FP7 grant agreement 282510))National Cancer Institute (U.S.) (Physical Sciences Oncology Center at MIT, U54CA143874
