BASH: a tool for managing BeadArray spatial artefacts. - Jonathan M. Cairns; Mark J. Dunning; Matthew E. Ritchie; Roslin Russell; Andy G. Lynch (Bioinform., 2008)

BayesPeak - an R package for analysing ChIP-seq data. - Jonathan M. Cairns; Christiana Spyrou; Rory Stark; Mike L. Smith; Andy G. Lynch; Simon Tavaré (Bioinform., 2011)

Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data. - Jonathan M. Cairns; William R. Orchard; Valeriya Malysheva; Mikhail Spivakov (Bioinform., 2019)