title: A locally convoluted cluster model for nucleosome positioning signals in chemical map.
abstract: Nucleosome is the fundamental packing unit of DNA in eukaryotic cells, and its positioning plays a critical role in regulation of gene expression and chromosome functions. Using a recently developed chemical mapping method, nucleosomes can be potentially mapped with an unprecedented single-base-pair resolution. Existence of overlapping nucleosomes due to cell mixture or cell dynamics, however, causes convolution of nucleosome positioning signals. In this paper, we introduce a locally convoluted cluster model and a maximum likelihood deconvolution approach, and illustrate the effectiveness of this approach in quantification of the nucleosome positional signal in the chemical mapping data.
authors.affiliation: Department of Statistics, Northwestern University, IL 60208, USA.
authors.forename: Liqun
authors.initials: L
authors.lastname: Xi
authors.affiliation: Department of Molecular Biosciences, Northwestern University, IL 60208, USA.
authors.forename: Kristin
authors.initials: K
authors.lastname: Brogaard
authors.affiliation: Department of Statistics, Northwestern University, IL 60208, USA.
authors.forename: Qingyang
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Department of Statistics, The Pennsylvania State University, PA, 16802.
authors.forename: Bruce
authors.initials: B
authors.lastname: Lindsay
authors.affiliation: Department of Molecular Biosciences, Northwestern University, IL 60208, USA.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Widom
authors.affiliation: Department of Statistics, Northwestern University, IL 60208, USA ; Department of Molecular Biosciences, Northwestern University, IL 60208, USA.
authors.forename: Ji-Ping
authors.initials: JP
authors.lastname: Wang
keywords: Chemical mapping; Deconvolution; EM algorithm; Negative Binomial cluster model; Nucleosome positioning; Poisson cluster model