Sanjaya, Maljanen, Katainen, Waszak, Genomics England Research Consortium, Aaltonen, Stegle, Korbel, Pitkänen. Mutation-Attention (MuAt): deep representation learning of somatic mutations for tumour typing and subtyping. Genome Medicine 15:47 (2023). doi:10.1186/s13073-023-01204-4. [bioRxiv preprint]
Timonen, Kerkelä, Impola, Penna, Partanen, Kilpivaara, Arvas, Pitkänen. DeepIFC: virtual fluorescent labeling of blood cells in imaging flow cytometry data with deep learning. Cytometry Part A (2023). doi:10.1002/cyto.a.24770 [bioRxiv preprint]
Pohjonen, Stürenberg, Rannikko*, Mirtti*, Pitkänen*, Spectral decoupling for training transferable neural networks in medical imaging. iScience 25, 2 (2022). doi: 10.1016/j.isci.2022.103767 [arXiv preprint]
The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Pan-cancer analysis of whole genomes. Nature 578, 82-93 (2020). doi: 10.1038/s41586-020-1969-6.
Katainen, Donner, Cajuso, Kaasinen, Palin, Mäkinen, Aaltonen, Pitkänen, Discovery of potential causative mutations in human coding and noncoding genome with the interactive software BasePlayer. Nature Protocols 13, 2580 (2018). doi: 10.1038/s41596-018-0052-3.
Palin*, Pitkänen*, Turunen*, Sahu*, Pihlajamaa*, Kivioja*, Kaasinen*, Välimäki, Hänninen, Cajuso, Aavikko, Tuupanen, Kilpivaara, Berg, Kondelin, Tanskanen, Katainen, Grau, Rauanheimo, Plaketti, Taira, Sulo, Hartonen, Dave, Schmierer, Botla, Sokolova, Vähärautio, Gladysz, Ongen, Dermitzakis, Bramsen, Ørntoft, Andersen, Ristimäki, Lepistö, Renkonen-Sinisalo, Mecklin, Taipale & Aaltonen, Contribution of allelic imbalance to colorectal cancer. Nature Communications 9, 3664 (2018). doi: 10.1038/s41467-018-06132-1.
Kondelin, Gylfe, Lundgren, Tanskanen, Hamberg, Aavikko, Palin, Ristolainen, Katainen, Kaasinen, Taipale, Taipale, Renkonen-Sinisalo, Järvinen, Böhm, Mecklin, Vahteristo, Tuupanen, Aaltonen, Pitkänen, Comprehensive evaluation of protein coding mononucleotide microsatellites in microsatellite-unstable colorectal cancer. Cancer Research 77, 4078–4088 (2017). doi: 10.1158/0008-5472.CAN-17-0682.
Katainen*, Dave*, Pitkänen*, Palin*, Kivioja, Välimäki, Gylfe, Ristolainen, Hänninen, Cajuso, Kondelin, Tanskanen, Mecklin, Järvinen, Renkonen-Sinisalo, Lepistö, Kaasinen, Kilpivaara, Tuupanen, Enge, Taipale, Aaltonen, CTCF/cohesin-binding sites are frequently mutated in cancer. Nature Genetics 47, 818 (2015). doi: 10.1038/ng.3335.
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