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)

qSNE: quadratic rate t-SNE optimizer with automatic parameter tuning for large datasets. - Antti Häkkinen; Juha Koiranen; Julia Casado; Katja Kaipio; Oskari Lehtonen; Eleonora Petrucci; Johanna Hynninen; Sakari Hietanen; Olli Carpén; Luca Pasquini; Mauro Biffoni; Rainer Lehtonen; et al. (Bioinform., 2020)

Agile workflow for interactive analysis of mass cytometry data. - Julia Casado; Oskari Lehtonen; Ville Rantanen; Katja Kaipio; Luca Pasquini; Antti Häkkinen; Elenora Petrucci; Johanna Hynninen; Sakari Hietanen; Olli Carpén; Mauro Biffoni; Anniina Färkkilä; et al. (Bioinform., 2021)

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)