BINOCh: binding inference from nucleosome occupancy changes

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


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.

Availability: The BINOCh open source Python package is freely available at under the FreeBSD license.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Cell Line, Tumor
  • Dihydrotestosterone / metabolism
  • Histones / metabolism
  • Humans
  • Nucleosomes / metabolism*
  • Oligonucleotide Array Sequence Analysis
  • Receptors, Androgen / metabolism
  • Software*
  • Transcription Factors / metabolism*


  • Histones
  • Nucleosomes
  • Receptors, Androgen
  • Transcription Factors
  • Dihydrotestosterone