Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays. - Marko Laakso; Sari Tuupanen; Auli Karhu; Rainer Lehtonen; Lauri A. Aaltonen; Sampsa Hautaniemi (Bioinform., 2007)

Lep-MAP: fast and accurate linkage map construction for large SNP datasets. - Pasi Rastas; Lars Paulin; Ilkka Hanski; Rainer Lehtonen; Petri Auvinen (Bioinform., 2013)

SePIA: RNA and small RNA sequence processing, integration, and analysis. - Katherine Icay; Ping Chen; Alejandra Cervera; Ville Rantanen; Rainer Lehtonen; Sampsa Hautaniemi (BioData Min., 2016)

Data integration to prioritize drugs using genomics and curated data. - Riku Louhimo; Marko Laakso; Denis Belitskin; Juha Klefström; Rainer Lehtonen; Sampsa Hautaniemi (BioData Min., 2016)

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)

PerPAS: Topology-Based Single Sample Pathway Analysis Method. - Chengyu Liu 002; Rainer Lehtonen; Sampsa Hautaniemi (IEEE ACM Trans. Comput. Biol. 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)

FUNGI: FUsioN Gene Integration toolset. - Alejandra Cervera; Heidi Rausio; Tiia Kähkönen; Noora Andersson; Gabriele Partel; Ville Rantanen; Giulia Paciello; Elisa Ficarra; Johanna Hynninen; Sakari Hietanen; Olli Carpén; Rainer Lehtonen; 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)