2023
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- 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.
- 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.
- 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.
- 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 .
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- 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.
- 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 .
- 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 .
- 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.
- 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.
- 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.
- 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.
- 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.
2022
- 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.
- 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.
- 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.
- 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.
- 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.
- 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 .
- 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.
- 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.
- 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 .
- 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 .
- 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.
- 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 .