dc.contributor.author | Fudenberg, Geoffrey | |
dc.contributor.author | McCord, Rachel P. | |
dc.contributor.author | Naumova, Natalia | |
dc.contributor.author | Goloborodko, Anton | |
dc.contributor.author | Lajoie, Bryan R | |
dc.contributor.author | Dekker, Job | |
dc.contributor.author | Imakaev, Maksim Viktorovich | |
dc.contributor.author | Mirny, Leonid A. | |
dc.date.accessioned | 2015-01-20T14:30:31Z | |
dc.date.available | 2015-01-20T14:30:31Z | |
dc.date.issued | 2012-09 | |
dc.date.submitted | 2012-05 | |
dc.identifier.issn | 1548-7091 | |
dc.identifier.issn | 1548-7105 | |
dc.identifier.uri | http://hdl.handle.net/1721.1/92953 | |
dc.description.abstract | Extracting biologically meaningful information from chromosomal interactions obtained with genome-wide chromosome conformation capture (3C) analyses requires the elimination of systematic biases. We present a computational pipeline that integrates a strategy to map sequencing reads with a data-driven method for iterative correction of biases, yielding genome-wide maps of relative contact probabilities. We validate this ICE (iterative correction and eigenvector decomposition) technique on published data obtained by the high-throughput 3C method Hi-C, and we 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_US |
dc.description.sponsorship | National Cancer Institute (U.S.). Physical Sciences-Oncology Center (U54CA143874) | en_US |
dc.language.iso | en_US | |
dc.publisher | Nature Publishing Group | en_US |
dc.relation.isversionof | http://dx.doi.org/10.1038/nmeth.2148 | en_US |
dc.rights | Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. | en_US |
dc.source | PMC | en_US |
dc.title | Iterative correction of Hi-C data reveals hallmarks of chromosome organization | en_US |
dc.type | Article | en_US |
dc.identifier.citation | Imakaev, Maxim, Geoffrey Fudenberg, Rachel Patton McCord, Natalia Naumova, Anton Goloborodko, Bryan R Lajoie, Job Dekker, and Leonid A Mirny. “Iterative Correction of Hi-C Data Reveals Hallmarks of Chromosome Organization.” Nature Methods 9, no. 10 (September 2, 2012): 999–1003. | en_US |
dc.contributor.department | Institute for Medical Engineering and Science | en_US |
dc.contributor.department | Massachusetts Institute of Technology. Department of Physics | en_US |
dc.contributor.mitauthor | Imakaev, Maksim Viktorovich | en_US |
dc.contributor.mitauthor | Goloborodko, Anton | en_US |
dc.contributor.mitauthor | Mirny, Leonid A. | en_US |
dc.relation.journal | Nature Methods | en_US |
dc.eprint.version | Author's final manuscript | en_US |
dc.type.uri | http://purl.org/eprint/type/JournalArticle | en_US |
eprint.status | http://purl.org/eprint/status/PeerReviewed | en_US |
dspace.orderedauthors | Imakaev, Maxim; Fudenberg, Geoffrey; McCord, Rachel Patton; Naumova, Natalia; Goloborodko, Anton; Lajoie, Bryan R; Dekker, Job; Mirny, Leonid A | en_US |
dc.identifier.orcid | https://orcid.org/0000-0002-0785-5410 | |
dc.identifier.orcid | https://orcid.org/0000-0002-5320-2728 | |
dc.identifier.orcid | https://orcid.org/0000-0002-2210-8616 | |
mit.license | PUBLISHER_POLICY | en_US |
mit.metadata.status | Complete | |