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Computational Biology

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

Publications

2023

  1. Kaljunen, H, Taavitsainen, S, Kaarijärvi, R, Takala, E, Paakinaho, V, Nykter, M et al.. Fanconi anemia pathway regulation by FANCI in prostate cancer. Front Oncol. 2023;13 :1260826. doi: 10.3389/fonc.2023.1260826. PubMed PMID:38023254 PubMed Central PMC10643534.
  2. Lin, J, Moradi, E, Salenius, K, Lehtipuro, S, Häkkinen, T, Laiho, JE et al.. Distinct transcriptomic profiles in children prior to the appearance of type 1 diabetes-linked islet autoantibodies and following enterovirus infection. Nat Commun. 2023;14 (1):7630. doi: 10.1038/s41467-023-42763-9. PubMed PMID:37993433 PubMed Central PMC10665402.
  3. Rautajoki, KJ, Jaatinen, S, Hartewig, A, Tiihonen, AM, Annala, M, Salonen, I et al.. Genomic characterization of IDH-mutant astrocytoma progression to grade 4 in the treatment setting. Acta Neuropathol Commun. 2023;11 (1):176. doi: 10.1186/s40478-023-01669-9. PubMed PMID:37932833 PubMed Central PMC10629206.
  4. Nurminen, A, Jaatinen, S, Taavitsainen, S, Högnäs, G, Lesluyes, T, Ansari-Pour, N et al.. Cancer origin tracing and timing in two high-risk prostate cancers using multisample whole genome analysis: prospects for personalized medicine. Genome Med. 2023;15 (1):82. doi: 10.1186/s13073-023-01242-y. PubMed PMID:37828555 PubMed Central PMC10571458.
  5. Sumiyoshi, T, Wang, X, Warner, EW, Sboner, A, Annala, M, Sigouros, M et al.. Molecular features of prostate cancer post-neoadjuvant therapy in the Phase 3 CALGB 90203 trial. J Natl Cancer Inst. 2023; :. doi: 10.1093/jnci/djad184. PubMed PMID:37676819 .
  6. Sattari, M, Kohvakka, A, Moradi, E, Rauhala, H, Urhonen, H, Isaacs, WB et al.. Identification of long noncoding RNAs with aberrant expression in prostate cancer metastases. Endocr Relat Cancer. 2023;30 (8):. doi: 10.1530/ERC-22-0247. PubMed PMID:37140987 PubMed Central PMC10326635.
  7. Hamis, S, Somervuo, P, Ågren, JA, Tadele, DS, Kesseli, J, Scott, JG et al.. Spatial cumulant models enable spatially informed treatment strategies and analysis of local interactions in cancer systems. J Math Biol. 2023;86 (5):68. doi: 10.1007/s00285-023-01903-x. PubMed PMID:37017776 PubMed Central PMC10076412.
  8. Ojanen, MJT, Caro, FM, Aittomäki, S, Ploquin, MJ, Ortutay, Z, Pekkarinen, M et al.. FURIN regulates cytotoxic T-lymphocyte effector function and memory cell transition in mice. Eur J Immunol. 2023;53 (6):e2250246. doi: 10.1002/eji.202250246. PubMed PMID:37015057 .
  9. Tolmeijer, SH, Boerrigter, E, Sumiyoshi, T, Kwan, EM, Ng, SWS, Annala, M et al.. Early On-treatment Changes in Circulating Tumor DNA Fraction and Response to Enzalutamide or Abiraterone in Metastatic Castration-Resistant Prostate Cancer. Clin Cancer Res. 2023;29 (15):2835-2844. doi: 10.1158/1078-0432.CCR-22-2998. PubMed PMID:36996325 .
  10. Alanen, E, Heikkinen, S, Nurminen, R, Nykter, M, Haapasalo, H, Hirvonen, E et al.. Early-onset grade 2-3 diffuse gliomas and schwannomas increase the risk of central nervous system tumors among the patients’ relatives. Neurooncol Adv. 2023;5 (1):vdad008. doi: 10.1093/noajnl/vdad008. PubMed PMID:36950216 PubMed Central PMC10025807.
  11. Severson, TM, Zhu, Y, Prekovic, S, Schuurman, K, Nguyen, HM, Brown, LG et al.. Enhancer profiling identifies epigenetic markers of endocrine resistance and reveals therapeutic options for metastatic castration-resistant prostate cancer patients. medRxiv. 2023; :. doi: 10.1101/2023.02.24.23286403. PubMed PMID:36865297 PubMed Central PMC9980263.
  12. Aakula, A, Sharma, M, Tabaro, F, Nätkin, R, Kamila, J, Honkanen, H et al.. RAS and PP2A activities converge on epigenetic gene regulation. Life Sci Alliance. 2023;6 (5):. doi: 10.26508/lsa.202301928. PubMed PMID:36858798 PubMed Central PMC9979842.
  13. 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 PubMed Central PMC9942993.
  14. 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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