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Computational Biology

We are part of Academy of Finland Center of Excellence in Tumor Genetics

Publications

2025

  1. Krossa, S, Andersen, MK, Sandholm, EM, Wess, M, Kiviaho, A, Sharma, A et al.. Spatial multi-omics identifies aggressive prostate cancer signatures highlighting pro-inflammatory chemokine activity in the tumor microenvironment. Nat Commun. 2025;16 (1):10160. doi: 10.1038/s41467-025-65161-9. PubMed PMID:41258098 PubMed Central PMC12630738.
  2. De Marco, L, Micarelli, E, Panula, J, Nikkola, J, Moilanen, L, Annala, M et al.. NOUS-209 off-the-shelf immunotherapy has the potential to hit primary and metachronous colorectal and urothelial cancer in Lynch syndrome. Mol Cancer Ther. 2025; :. doi: 10.1158/1535-7163.MCT-25-0864. PubMed PMID:41232028 .
  3. Virtanen, T, Kwan, EM, Parekh, K, Bacon, JVW, Huang, CF, Yu, IPL et al.. Repertoire and clinical hierarchy of AR locus alterations in castration-resistant prostate cancer. Ann Oncol. 2025; :. doi: 10.1016/j.annonc.2025.10.1236. PubMed PMID:41161480 .
  4. Nikkola, J, Ryyppö, L, Vuorinen, J, Moilanen, L, Ahtiainen, M, Pylvänäinen, K et al.. Constrained hypermutation and absence of TERT promoter mutations in Lynch syndrome-associated urothelial cancer. Cell Rep. 2025;44 (10):116388. doi: 10.1016/j.celrep.2025.116388. PubMed PMID:41046515 .
  5. Hormalainen, K, Marttila, K, Nykter, M, Uibu, T, Ahvonen, J, Fey, V et al.. Comprehensive Genomic Profiling in Advanced Non-Small Cell Lung Cancer: A Real-World Cohort Study in Finland. Cancer Med. 2025;14 (19):e71250. doi: 10.1002/cam4.71250. PubMed PMID:41015991 PubMed Central PMC12476845.
  6. Severson, TM, Minnee, E, Zhu, Y, Schuurman, K, Nguyen, HM, Brown, LG et al.. Epigenetic profiling identifies markers of endocrine resistance and therapeutic options for metastatic castration-resistant prostate cancer. Cell Rep Med. 2025;6 (7):102215. doi: 10.1016/j.xcrm.2025.102215. PubMed PMID:40609538 PubMed Central PMC12281433.
  7. Vandekerkhove, G, Murtha, AJ, Müller, DC, Stephenson, M, Rostin, K, Munzur, AD et al.. ERBB2/HER2 Alterations in ctDNA and Metachronous Tissues of Patients with Metastatic Urothelial Cancer. Clin Cancer Res. 2025;31 (17):3725-3741. doi: 10.1158/1078-0432.CCR-24-3912. PubMed PMID:40540011 .
  8. Sattari, M, Rauhala, H, Latonen, L, Isaacs, WB, Nykter, M, Bova, GS et al.. Identification of protein-coding genes associated with metastatic prostate cancer. Endocr Relat Cancer. 2025;32 (7):. doi: 10.1530/ERC-25-0070. PubMed PMID:40525903 PubMed Central PMC12203752.
  9. Kwan, EM, Ng, SWS, Tolmeijer, SH, Emmett, L, Sandhu, S, Buteau, JP et al.. Lutetium-177-PSMA-617 or cabazitaxel in metastatic prostate cancer: circulating tumor DNA analysis of the randomized phase 2 TheraP trial. Nat Med. 2025;31 (8):2722-2736. doi: 10.1038/s41591-025-03704-9. PubMed PMID:40425844 .
  10. Peterson, C, Tagoma, A, Alnek, K, Bärenson, A, Vorobjova, T, Talja, I et al.. Antibodies against in the children of mothers at risk for gestational diabetes. Immunol Med. 2025;48 (4):346-356. doi: 10.1080/25785826.2025.2504021. PubMed PMID:40406906 .
  11. Uusi-Mäkelä, J, Kauppinen, M, Seppälä, J, Jaatinen, S, Ryback, B, Rantapero, T et al.. Tumor-associated long non-coding RNAs show variable expression across diffuse gliomas and effect on cell growth upon silencing in glioblastoma. Sci Rep. 2025;15 (1):16220. doi: 10.1038/s41598-025-99984-9. PubMed PMID:40346283 PubMed Central PMC12064817.
  12. Uusi-Mäkelä, M, Harjula, SE, Junno, M, Sillanpää, A, Nätkin, R, Niskanen, MT et al.. The inflammasome adaptor pycard is essential for immunity against Mycobacterium marinum infection in adult zebrafish. Dis Model Mech. 2025;18 (9):. doi: 10.1242/dmm.052061. PubMed PMID:39916610 PubMed Central PMC11972081.
  13. Hermelo, I, Virtanen, T, Salonen, I, Nätkin, R, Keitaanniemi, S, Tiihonen, AM et al.. Unsupervised clustering reveals noncanonical myeloid cell subsets in the brain tumor microenvironment. Cancer Immunol Immunother. 2025;74 (2):63. doi: 10.1007/s00262-024-03920-1. PubMed PMID:39751910 PubMed Central PMC11699035.
  14. Sipola, J, Munzur, AD, Kwan, EM, Seo, CCY, Hauk, BJ, Parekh, K et al.. Plasma Cell-Free DNA Chromatin Immunoprecipitation Profiling Depicts Phenotypic and Clinical Heterogeneity in Advanced Prostate Cancer. Cancer Res. 2025;85 (4):791-807. doi: 10.1158/0008-5472.CAN-24-2052. PubMed PMID:39652574 PubMed Central PMC11832346.
  15. Hermelo, I, Haapala, I, Mäkelä, M, Jacome Sanz, D, Kontunen, A, Karjalainen, M et al.. Patient-derived glioma organoids real time identification of IDH mutation, 1p/19q-codeletion and CDKN2A/B homozygous deletion with differential ion mobility spectrometry. J Neurooncol. 2025;171 (3):691-703. doi: 10.1007/s11060-024-04891-0. PubMed PMID:39578301 PubMed Central PMC11729090.
  16. Nikkola, J, Ryyppö, L, Vuorinen, J, Kallio, H, Selin, H, Jämsä, P et al.. Sensitive Detection of Urothelial Cancer via High-volume Urine DNA Analysis. Eur Urol. 2025;87 (1):86-88. doi: 10.1016/j.eururo.2024.10.014. PubMed PMID:39443274 .

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