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Bioinformatics. 2011 Jul 1;27(13):1867-8. doi: 10.1093/bioinformatics/btr279. Epub 2011 May 5.

BINOCh: binding inference from nucleosome occupancy changes.

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  • 1Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA. cliff@jimmy.harvard.edu


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.


The BINOCh open source Python package is freely available at http://liulab.dfci.harvard.edu/BINOCh under the FreeBSD license.

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