Imakaev, MaximFudenberg, GeoffreyMcCord, Rachel PattonNaumova, NataliaGoloborodko, AntonLajoie, Bryan R.Dekker, JobMirny, Leonid2014-03-112013Imakaev, Maxim, Geoffrey Fudenberg, Rachel Patton McCord, Natalia Naumova, Anton Goloborodko, Bryan R. Lajoie, Job Dekker, and Leonid A Mirny. 2013. “Iterative Correction of Hi-C Data Reveals Hallmarks of Chromosome Organization.” Nature methods 9 (10): 10.1038/nmeth.2148. doi:10.1038/nmeth.2148. http://dx.doi.org/10.1038/nmeth.2148.1548-7091http://nrs.harvard.edu/urn-3:HUL.InstRepos:11878982Extracting biologically meaningful information from chromosomal interactions obtained with genome-wide chromosome conformation capture (3C) analyses requires elimination of systematic biases. We present a pipeline that integrates a strategy for mapping of sequencing reads and a data-driven method for iterative correction of biases, yielding genome-wide maps of relative contact probabilities. We validate ICE (Iterative Correction and Eigenvector decomposition) on published Hi-C data, and demonstrate that eigenvector decomposition of the obtained maps provides insights into local chromatin states, global patterns of chromosomal interactions, and the conserved organization of human and mouse chromosomes.en-USJournal Article2014-03-1110.1038/nmeth.2148