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Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit.
Lavikka K, Oikkonen J, Li Y, Muranen T, Micoli G, Marchi G, Lahtinen A, Huhtinen K, Lehtonen R, Hietanen S, Hynninen J, Virtanen A, Hautaniemi S. Lavikka K, et al. Among authors: lehtonen r. Gigascience. 2024 Jan 2;13:giae040. doi: 10.1093/gigascience/giae040. Gigascience. 2024. PMID: 39101783 Free PMC article.
qSNE: quadratic rate t-SNE optimizer with automatic parameter tuning for large datasets.
Häkkinen A, Koiranen J, Casado J, Kaipio K, Lehtonen O, Petrucci E, Hynninen J, Hietanen S, Carpén O, Pasquini L, Biffoni M, Lehtonen R, Hautaniemi S. Häkkinen A, et al. Among authors: lehtonen o, lehtonen r. Bioinformatics. 2020 Dec 22;36(20):5086-5092. doi: 10.1093/bioinformatics/btaa637. Bioinformatics. 2020. PMID: 32663244 Free PMC article.
Prospective Longitudinal ctDNA Workflow Reveals Clinically Actionable Alterations in Ovarian Cancer.
Oikkonen J, Zhang K, Salminen L, Schulman I, Lavikka K, Andersson N, Ojanperä E, Hietanen S, Grénman S, Lehtonen R, Huhtinen K, Carpén O, Hynninen J, Färkkilä A, Hautaniemi S. Oikkonen J, et al. Among authors: lehtonen r. JCO Precis Oncol. 2019 May 3;3:PO.18.00343. doi: 10.1200/PO.18.00343. eCollection 2019. JCO Precis Oncol. 2019. PMID: 32914024 Free PMC article.
PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples.
Häkkinen A, Zhang K, Alkodsi A, Andersson N, Erkan EP, Dai J, Kaipio K, Lamminen T, Mansuri N, Huhtinen K, Vähärautio A, Carpén O, Hynninen J, Hietanen S, Lehtonen R, Hautaniemi S. Häkkinen A, et al. Among authors: lehtonen r. Bioinformatics. 2021 Sep 29;37(18):2882-2888. doi: 10.1093/bioinformatics/btab178. Bioinformatics. 2021. PMID: 33720334 Free PMC article.
Computational identification of cancer susceptibility loci.
Laakso M, Karinen S, Lehtonen R, Hautaniemi S. Laakso M, et al. Among authors: lehtonen r. Methods Mol Biol. 2010;653:87-103. doi: 10.1007/978-1-60761-759-4_6. Methods Mol Biol. 2010. PMID: 20721739 Review.
A Functional Homologous Recombination Assay Predicts Primary Chemotherapy Response and Long-Term Survival in Ovarian Cancer Patients.
Tumiati M, Hietanen S, Hynninen J, Pietilä E, Färkkilä A, Kaipio K, Roering P, Huhtinen K, Alkodsi A, Li Y, Lehtonen R, Erkan EP, Tuominen MM, Lehti K, Hautaniemi SK, Vähärautio A, Grénman S, Carpén O, Kauppi L. Tumiati M, et al. Among authors: lehtonen r. Clin Cancer Res. 2018 Sep 15;24(18):4482-4493. doi: 10.1158/1078-0432.CCR-17-3770. Epub 2018 Jun 1. Clin Cancer Res. 2018. PMID: 29858219
Identifying differentially methylated sites in samples with varying tumor purity.
Häkkinen A, Alkodsi A, Facciotto C, Zhang K, Kaipio K, Leppä S, Carpén O, Grénman S, Hynninen J, Hietanen S, Lehtonen R, Hautaniemi S. Häkkinen A, et al. Among authors: lehtonen r. Bioinformatics. 2018 Sep 15;34(18):3078-3085. doi: 10.1093/bioinformatics/bty310. Bioinformatics. 2018. PMID: 29912358
86 results