title: BINOCh: binding inference from nucleosome occupancy changes.
abstract: Transcription factor binding events are frequently associated with a pattern of nucleosome occupancy changes in which nucleosomes flanking the binding site increase in occupancy, while those in the vicinity of the binding site itself are displaced. Genome-wide information on enhancer proximal nucleosome occupancy can be readily acquired using ChIP-seq targeting enhancer-related histone modifications such as H3K4me2. Here, we present a software package, BINOCh that allows biologists to use such data to infer the identity of key transcription factors that regulate the response of a cell to a stimulus or determine a program of differentiation.
  
  
  BACKGROUND
  The BINOCh open source Python package is freely available at http://liulab.dfci.harvard.edu/BINOCh under the FreeBSD license.
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA. cliff@jimmy.harvard.edu
authors.forename: Clifford A
authors.initials: CA
authors.lastname: Meyer
authors.forename: Housheng H
authors.initials: HH
authors.lastname: He
authors.forename: Myles
authors.initials: M
authors.lastname: Brown
authors.forename: X Shirley
authors.initials: XS
authors.lastname: Liu
mesh_terms: D045744:Cell Line, Tumor; D013196:Dihydrotestosterone / Q000378:metabolism; D006657:Histones / Q000378:metabolism; D006801:Humans; D009707:Nucleosomes / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D011944:Receptors, Androgen / Q000378:metabolism; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D006657:Histones; D009707:Nucleosomes; D011944:Receptors, Androgen; D014157:Transcription Factors; D013196:Dihydrotestosterone