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Computational Biology

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

Publications

2024

  1. Salenius, K, Väljä, N, Thusberg, S, Iris, F, Ladd-Acosta, C, Roos, C et al.. Exploring autism spectrum disorder and co-occurring trait associations to elucidate multivariate genetic mechanisms and insights. BMC Psychiatry. 2024;24 (1):934. doi: 10.1186/s12888-024-06392-w. PubMed PMID:39696186 .
  2. 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. 2024; :. doi: 10.1158/0008-5472.CAN-24-2052. PubMed PMID:39652574 .
  3. 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. 2024; :. doi: 10.1007/s11060-024-04891-0. PubMed PMID:39578301 .
  4. Kiviaho, A, Eerola, SK, Kallio, HML, Andersen, MK, Hoikka, M, Tiihonen, AM et al.. Single cell and spatial transcriptomics highlight the interaction of club-like cells with immunosuppressive myeloid cells in prostate cancer. Nat Commun. 2024;15 (1):9949. doi: 10.1038/s41467-024-54364-1. PubMed PMID:39550375 PubMed Central PMC11569175.
  5. 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 .
  6. Kukkonen-Macchi, A, Hautaniemi, S, Heil, KF, Heinäniemi, M, Jensen, LJ, Junttila, S et al.. ECCB2024: The 23rd European Conference on Computational Biology. Bioinformatics. 2024;40 (Suppl 2):ii1-ii3. doi: 10.1093/bioinformatics/btae422. PubMed PMID:39230712 PubMed Central PMC11373319.
  7. Hakola, L, Lund-Blix, NA, Takkinen, HM, Tapanainen, H, Niinistö, S, Korhonen, TE et al.. Maternal gluten, cereal, and dietary fiber intake during pregnancy and lactation and the risk of islet autoimmunity and type 1 diabetes in the child. Clin Nutr ESPEN. 2024;62 :22-27. doi: 10.1016/j.clnesp.2024.05.001. PubMed PMID:38901945 .
  8. Nurminen, R, Afyounian, E, Paunu, N, Katainen, R, Isomäki, M, Nurminen, A et al.. Previously reported CCDC26 risk variant and novel germline variants in GALNT13, AR, and MYO10 associated with familial glioma in Finland. Sci Rep. 2024;14 (1):11562. doi: 10.1038/s41598-024-62296-5. PubMed PMID:38773237 PubMed Central PMC11109329.
  9. Kallio, HM, Savolainen, K, Virtanen, T, Ryyppö, L, Selin, H, Martikainen, P et al.. Sensitive circulating tumor DNA-based residual disease detection in epithelial ovarian cancer. Life Sci Alliance. 2024;7 (6):. doi: 10.26508/lsa.202402658. PubMed PMID:38580393 PubMed Central PMC10997860.
  10. Pekkarinen, M, Nordfors, K, Uusi-Mäkelä, J, Kytölä, V, Hartewig, A, Huhtala, L et al.. Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors. Life Sci Alliance. 2024;7 (6):. doi: 10.26508/lsa.202302088. PubMed PMID:38499326 PubMed Central PMC10948937.
  11. Fonseca, NM, Maurice-Dror, C, Herberts, C, Tu, W, Fan, W, Murtha, AJ et al.. Prediction of plasma ctDNA fraction and prognostic implications of liquid biopsy in advanced prostate cancer. Nat Commun. 2024;15 (1):1828. doi: 10.1038/s41467-024-45475-w. PubMed PMID:38418825 PubMed Central PMC10902374.
  12. Kivioja, T, Posti, JP, Sipilä, J, Rauhala, M, Frantzén, J, Gardberg, M et al.. Motor dysfunction as a primary symptom predicts poor outcome: multicenter study of glioma symptoms. Front Oncol. 2023;13 :1305725. doi: 10.3389/fonc.2023.1305725. PubMed PMID:38239655 PubMed Central PMC10794640.
  13. Warner, EW, Van der Eecken, K, Murtha, AJ, Kwan, EM, Herberts, C, Sipola, J et al.. Multiregion sampling of de novo metastatic prostate cancer reveals complex polyclonality and augments clinical genotyping. Nat Cancer. 2024;5 (1):114-130. doi: 10.1038/s43018-023-00692-y. PubMed PMID:38177459 .
  14. Sumiyoshi, T, Wang, X, Warner, EW, Sboner, A, Annala, M, Sigouros, M et al.. Molecular features of prostate cancer after neoadjuvant therapy in the phase 3 CALGB 90203 trial. J Natl Cancer Inst. 2024;116 (1):115-126. doi: 10.1093/jnci/djad184. PubMed PMID:37676819 PubMed Central PMC10777679.

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