CGH-Plotter: MATLAB toolbox for CGH-data analysis. - Reija Autio; Sampsa Hautaniemi; Päivikki Kauraniemi; Olli Yli-Harja; Jaakko Astola; Maija Wolf; Anne Kallioniemi (Bioinform., 2003)

A strategy for identifying putative causes of gene expression variation in human cancers. - Sampsa Hautaniemi; Markus Ringnér; Päivikki Kauraniemi; Reija Autio; Henrik Edgren; Olli Yli-Harja; Jaakko Astola; Anne Kallioniemi; Olli-Pekka Kallioniemi (J. Frankl. Inst., 2004)

Comparison of Affymetrix data normalization methods using 6, 926 experiments across five array generations. - Reija Autio; Sami Kilpinen; Matti Saarela; Olli-P. Kallioniemi; Sampsa Hautaniemi; Jaakko Astola (BMC Bioinform., 2009)

Advanced analysis and visualization of gene copy number and expression data. - Reija Autio; Matti Saarela; Anna-Kaarina Järvinen; Sampsa Hautaniemi; Jaakko Astola (BMC Bioinform., 2009)

DBComposer: An R package for integrative analysis and management of gene expression microarray data. - Lingjia Kong; Kaisa-Leena Aho; Kirsi Granberg; Christophe Roos; Reija Autio (GENSiPS, 2013)

Integrative genomics and transcriptomics analysis of human embryonic and induced pluripotent stem cells. - Kirsti Laurila; Reija Autio; Lingjia Kong; Elisa Närvä; Samer Hussein; Timo Otonkoski; Riitta Lahesmaa; Harri Lähdesmäki (BioData Min., 2014)