Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data. - Amjad Alkodsi; Riku Louhimo; Sampsa Hautaniemi (Briefings Bioinform., 2015)

Identifying differentially methylated sites in samples with varying tumor purity. - Antti Häkkinen; Amjad Alkodsi; Chiara Facciotto; Kaiyang Zhang; Katja Kaipio; Sirpa Leppä; Olli Carpén; Seija Grénman; Johanna Hynninen; Sakari Hietanen; Rainer Lehtonen; Sampsa Hautaniemi (Bioinform., 2018)

Anduril 2: upgraded large-scale data integration framework. - Alejandra Cervera; Ville Rantanen; Kristian Ovaska; Marko Laakso; Javier Nuñez-Fontarnau; Amjad Alkodsi; Julia Casado; Chiara Facciotto; Antti Häkkinen; Riku Louhimo; Sirkku Karinen; Kaiyang Zhang; et al. (Bioinform., 2019)

PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples. - Antti Häkkinen; Kaiyang Zhang; Amjad Alkodsi; Noora Andersson; Erdogan Pekcan Erkan; Jun Dai; Katja Kaipio; Tarja Lamminen; Naziha Mansuri; Kaisa Huhtinen; Anna Vähärautio; Olli Carpén; et al. (Bioinform., 2021)