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Computational Biology

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

Publications

2023

  1. Nätkin, R, Pennanen, P, Syvälä, H, Bläuer, M, Kesseli, J, Tammela, TLJ et al.. Adaptive and non-adaptive gene expression responses in prostate cancer during androgen deprivation. PLoS One. 2023;18 (2):e0281645. doi: 10.1371/journal.pone.0281645. PubMed PMID:36809527 .
  2. Saralahti, AK, Harjula, SE, Rantapero, T, Uusi-Mäkelä, MIE, Kaasinen, M, Junno, M et al.. Characterization of the innate immune response to Streptococcus pneumoniae infection in zebrafish. PLoS Genet. 2023;19 (1):e1010586. doi: 10.1371/journal.pgen.1010586. PubMed PMID:36622851 PubMed Central PMC9858863.

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2022

  1. Sjöström, M, Zhao, SG, Levy, S, Zhang, M, Ning, Y, Shrestha, R et al.. The 5-Hydroxymethylcytosine Landscape of Prostate Cancer. Cancer Res. 2022;82 (21):3888-3902. doi: 10.1158/0008-5472.CAN-22-1123. PubMed PMID:36251389 PubMed Central PMC9627125.
  2. Kukkonen, K, Autio-Kimura, B, Rauhala, H, Kesseli, J, Nykter, M, Latonen, L et al.. Nonmalignant AR-positive prostate epithelial cells and cancer cells respond differently to androgen. Endocr Relat Cancer. 2022;29 (12):717-733. doi: 10.1530/ERC-22-0108. PubMed PMID:36219867 PubMed Central PMC9644224.
  3. Buhigas, C, Warren, AY, Leung, WK, Whitaker, HC, Luxton, HJ, Hawkins, S et al.. The architecture of clonal expansions in morphologically normal tissue from cancerous and non-cancerous prostates. Mol Cancer. 2022;21 (1):183. doi: 10.1186/s12943-022-01644-3. PubMed PMID:36131292 PubMed Central PMC9494848.
  4. Rautajoki, KJ, Jaatinen, S, Tiihonen, AM, Annala, M, Vuorinen, EM, Kivinen, A et al.. PTPRD and CNTNAP2 as markers of tumor aggressiveness in oligodendrogliomas. Sci Rep. 2022;12 (1):14083. doi: 10.1038/s41598-022-14977-2. PubMed PMID:35982066 PubMed Central PMC9388569.
  5. Koivisto, M, Tolvanen, TA, Toimela, T, Miinalainen, I, Kiviaho, A, Kesseli, J et al.. Functional human cell-based vascularised cardiac tissue model for biomedical research and testing. Sci Rep. 2022;12 (1):13459. doi: 10.1038/s41598-022-17498-0. PubMed PMID:35931748 PubMed Central PMC9355975.
  6. Herberts, C, Annala, M, Sipola, J, Ng, SWS, Chen, XE, Nurminen, A et al.. Deep whole-genome ctDNA chronology of treatment-resistant prostate cancer. Nature. 2022;608 (7921):199-208. doi: 10.1038/s41586-022-04975-9. PubMed PMID:35859180 .
  7. L B Almeida, B, M Bahrudeen, MN, Chauhan, V, Dash, S, Kandavalli, V, Häkkinen, A et al.. The transcription factor network of E. coli steers global responses to shifts in RNAP concentration. Nucleic Acids Res. 2022;50 (12):6801-6819. doi: 10.1093/nar/gkac540. PubMed PMID:35748858 PubMed Central PMC9262627.
  8. Cao, S, Wang, JR, Ji, S, Yang, P, Dai, Y, Guo, S et al.. Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression. Nat Biotechnol. 2022;40 (11):1624-1633. doi: 10.1038/s41587-022-01342-x. PubMed PMID:35697807 PubMed Central PMC9646498.
  9. Fonseca, NM, Van der Eecken, K, Herberts, C, Verbeke, S, Ng, SWS, Lumen, N et al.. Genomic Features of Lung-Recurrent Hormone-Sensitive Prostate Cancer. JCO Precis Oncol. 2022;6 :e2100543. doi: 10.1200/PO.21.00543. PubMed PMID:35507889 .
  10. Rodriguez-Martinez, A, Vuorinen, EM, Shcherban, A, Uusi-Mäkelä, J, Rajala, NKM, Nykter, M et al.. Novel ZNF414 activity characterized by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data. Biochim Biophys Acta Gene Regul Mech. 2022;1865 (3):194811. doi: 10.1016/j.bbagrm.2022.194811. PubMed PMID:35318951 .
  11. Ruusuvuori, P, Valkonen, M, Kartasalo, K, Valkonen, M, Visakorpi, T, Nykter, M et al.. Spatial analysis of histology in 3D: quantification and visualization of organ and tumor level tissue environment. Heliyon. 2022;8 (1):e08762. doi: 10.1016/j.heliyon.2022.e08762. PubMed PMID:35128089 PubMed Central PMC8800033.
  12. Bacon, JVW, Müller, DC, Ritch, E, Annala, M, Dugas, SG, Herberts, C et al.. Somatic Features of Response and Relapse in Non-muscle-invasive Bladder Cancer Treated with Bacillus Calmette-Guérin Immunotherapy. Eur Urol Oncol. 2022;5 (6):677-686. doi: 10.1016/j.euo.2021.11.002. PubMed PMID:34895867 .

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