To cite CisGenome or our ChIP-seq analysis algorithms, please refer to:

1. Hongkai Ji, Hui Jiang, Wenxiu Ma, David S. Johnson, Richard M. Myers and Wing H.    Wong (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nature Biotechnology, 26: 1293-1300. doi:10.1038/nbt.1505 [link]


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

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

3. 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. [link]


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

4. 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. [link]

CisGenome References