To cite CisGenome, please cite the website:

 http://www.biostat.jhsph.edu/~hji/cisgenome/.

(We are currently preparing a manuscript about CisGenome)

 

To cite tiling array and motif analysis algorithms, please refer to:

1. Hongkai Ji and Wing H. Wong (2005) TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics, 21: 3629-3636.

2. Hongkai Ji, Steven A. Vokes and Wing H. Wong (2006) A comparative analysis of genome-wide chromatin immunoprecipitation data for mammalian transcription factors. Nucleic Acids Research, 34: e146. doi:10.1093/nar/gkl803.

 

If you performed de novo cis-regulatory module discovery using the CisModule function (under the menu “Motif > New Motif Discovery > CisModule”, please cite:

3. Qing Zhou and Wing H. Wong (2004) CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling. Proc. Natl. Acad. Sci. USA, 101: 12114-12119.

CisGenome References