Digital extractor: analysis of digital differential display output. - Stephen F. Madden; Barry O'Donovan; Simon J. Furney; Hugh R. Brady; Guenole C. M. Silvestre; Peter P. Doran (Bioinform., 2003)

Integrating transcription factor binding site information with gene expression datasets. - Ian B. Jeffery; Stephen F. Madden; Paul A. McGettigan; Guy Perrière; Aedín C. Culhane; Desmond G. Higgins (Bioinform., 2007)

Distinct Patterns in the Regulation and Evolution of Human Cancer Genes. - Simon J. Furney; Stephen F. Madden; Tomasz A. Kisiel; Desmond G. Higgins; Núria López-Bigas (Silico Biol., 2008)

Detecting microRNA activity from gene expression data. - Stephen F. Madden; Susan B. Carpenter; Ian B. Jeffery; Harry Björkbacka; Katherine A. Fitzgerald; Luke A. O'Neill; Desmond G. Higgins (BMC Bioinform., 2010)