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My students run a journal club that meets once a week and last Friday the paper we discussed was M. Imakaev et al., Iterative correction of Hi-C data reveals hallmarks of chromosome organization, Nature Methods 9 (2012), p 999–1003. The paper, from Leonid Mirny’s group, describes an approach to analyzing Hi-C data, and is one of only a few papers that have been published focusing on methods for this *Seq assay. Present at journal club were my students Nicolas Bray, Shannon Hateley, Harold Pimentel, Atif Rahman, Lorian Schaeffer, Akshay Tambe, Faraz Tavakoli, postdocs Sreeram Kannan and Shannon McCurdy, and guest Emily Brown from Doris Bachtrog’s group. They all read the paper prior to our meeting, and the notes below are a summary of our discussion (although I have taken some more time to flesh out the math for the interested reader). For those who are impatient, the bottom line is that I think the title of the paper by Imakaev et al. should have had a few extra words (mine in italics) so that it would be “Iterative proportional fitting of a log-linear model for correction of Hi-C data reveals hallmarks of chromosome organization”. Read the rest of this entry »

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