CanGEM: mining gene copy number changes in cancer. - Ilari Scheinin; Samuel Myllykangas; Ioana Borze; Tom Böhling; Sakari Knuutila; Juha Saharinen (Nucleic Acids Res., 2008)

CGHpower: exploring sample size calculations for chromosomal copy number experiments. - Ilari Scheinin; Jose A. Ferreira; Sakari Knuutila; Gerrit Meijer; Mark A. van de Wiel; Bauke Ylstra (BMC Bioinform., 2010)

Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma. - José Caldas; Nils Gehlenborg; Eeva Kettunen; Ali Faisal; Mikko Rönty; Andrew G. Nicholson; Sakari Knuutila; Alvis Brazma; Samuel Kaski (Bioinform., 2012)