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Computational Biology

Publications 2018

2018

  1. Annala, M, Taavitsainen, S, Vandekerkhove, G, Bacon, JVW, Beja, K, Chi, KN et al.. Frequent mutation of the untranslated region in prostate cancer. Commun Biol. 2018;1 :122. doi: 10.1038/s42003-018-0128-1. PubMed PMID:30272002 PubMed Central PMC6123809.
  2. Latonen, L, Nykter, M, Visakorpi, T. Proteomics of prostate cancer – revealing how cancer cells master their messy genomes. Oncoscience. 2018;5 (7-8):216-217. doi: 10.18632/oncoscience.453. PubMed PMID:30234142 PubMed Central PMC6142899.
  3. Lin, J, Kimura, BY, Oikarinen, S, Nykter, M. Bioinformatics Assembling and Assessment of Novel Coxsackievirus B1 Genome. Methods Mol Biol. 2018;1838 :261-272. doi: 10.1007/978-1-4939-8682-8_18. PubMed PMID:30129002 .
  4. Jylhä, A, Nättinen, J, Aapola, U, Mikhailova, A, Nykter, M, Zhou, L et al.. Comparison of iTRAQ and SWATH in a clinical study with multiple time points. Clin Proteomics. 2018;15 :24. doi: 10.1186/s12014-018-9201-5. PubMed PMID:30069167 PubMed Central PMC6065059.
  5. Veskimäe, K, Scaravilli, M, Niininen, W, Karvonen, H, Jaatinen, S, Nykter, M et al.. Expression Analysis of Platinum Sensitive and Resistant Epithelial Ovarian Cancer Patient Samples Reveals New Candidates for Targeted Therapies. Transl Oncol. 2018;11 (5):1160-1170. doi: 10.1016/j.tranon.2018.07.010. PubMed PMID:30056367 PubMed Central PMC6079561.
  6. Chedgy, EC, Vandekerkhove, G, Herberts, C, Annala, M, Donoghue, AJ, Sigouros, M et al.. Biallelic tumour suppressor loss and DNA repair defects in de novo small-cell prostate carcinoma. J Pathol. 2018;246 (2):244-253. doi: 10.1002/path.5137. PubMed PMID:30015382 .
  7. Kallio, HML, Hieta, R, Latonen, L, Brofeldt, A, Annala, M, Kivinummi, K et al.. Constitutively active androgen receptor splice variants AR-V3, AR-V7 and AR-V9 are co-expressed in castration-resistant prostate cancer metastases. Br J Cancer. 2018;119 (3):347-356. doi: 10.1038/s41416-018-0172-0. PubMed PMID:29988112 PubMed Central PMC6070921.
  8. Harjula, SE, Ojanen, MJT, Taavitsainen, S, Nykter, M, Rämet, M. Interleukin 10 mutant zebrafish have an enhanced interferon gamma response and improved survival against a Mycobacterium marinum infection. Sci Rep. 2018;8 (1):10360. doi: 10.1038/s41598-018-28511-w. PubMed PMID:29985419 PubMed Central PMC6037744.
  9. Luoto, S, Hermelo, I, Vuorinen, EM, Hannus, P, Kesseli, J, Nykter, M et al.. Computational Characterization of Suppressive Immune Microenvironments in Glioblastoma. Cancer Res. 2018;78 (19):5574-5585. doi: 10.1158/0008-5472.CAN-17-3714. PubMed PMID:29921698 .
  10. Nordfors, K, Haapasalo, J, Afyounian, E, Tuominen, J, Annala, M, Häyrynen, S et al.. Erratum: Whole-exome sequencing identifies germline mutation in and in a child with genomically aberrant AT/RT and her mother with anaplastic astrocytoma. Cold Spring Harb Mol Case Stud. 2018;4 (3):. doi: 10.1101/mcs.a003129. PubMed PMID:29858379 PubMed Central PMC5983177.
  11. Park, ES, Yan, JP, Ang, RA, Lee, JH, Deng, X, Duffy, SP et al.. Isolation and genome sequencing of individual circulating tumor cells using hydrogel encapsulation and laser capture microdissection. Lab Chip. 2018;18 (12):1736-1749. doi: 10.1039/c8lc00184g. PubMed PMID:29762619 .
  12. Kartasalo, K, Latonen, L, Vihinen, J, Visakorpi, T, Nykter, M, Ruusuvuori, P et al.. Comparative analysis of tissue reconstruction algorithms for 3D histology. Bioinformatics. 2018;34 (17):3013-3021. doi: 10.1093/bioinformatics/bty210. PubMed PMID:29684099 PubMed Central PMC6129300.
  13. Uusi-Mäkelä, MIE, Barker, HR, Bäuerlein, CA, Häkkinen, T, Nykter, M, Rämet, M et al.. Chromatin accessibility is associated with CRISPR-Cas9 efficiency in the zebrafish (Danio rerio). PLoS One. 2018;13 (4):e0196238. doi: 10.1371/journal.pone.0196238. PubMed PMID:29684067 PubMed Central PMC5912780.
  14. Gao, Q, Liang, WW, Foltz, SM, Mutharasu, G, Jayasinghe, RG, Cao, S et al.. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Rep. 2018;23 (1):227-238.e3. doi: 10.1016/j.celrep.2018.03.050. PubMed PMID:29617662 PubMed Central PMC5916809.
  15. Nordfors, K, Haapasalo, J, Afyounian, E, Tuominen, J, Annala, M, Häyrynen, S et al.. Whole-exome sequencing identifies germline mutation in and in a child with genomically aberrant AT/RT and her mother with anaplastic astrocytoma. Cold Spring Harb Mol Case Stud. 2018;4 (2):. doi: 10.1101/mcs.a002246. PubMed PMID:29602769 PubMed Central PMC5880256.
  16. Latonen, L, Afyounian, E, Jylhä, A, Nättinen, J, Aapola, U, Annala, M et al.. Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression. Nat Commun. 2018;9 (1):1176. doi: 10.1038/s41467-018-03573-6. PubMed PMID:29563510 PubMed Central PMC5862881.
  17. Haapasalo, J, Nordfors, K, Granberg, KJ, Kivioja, T, Nykter, M, Haapasalo, H et al.. NRF2, DJ1 and SNRX1 and their prognostic impact in astrocytic gliomas. Histol Histopathol. 2018;33 (8):791-801. doi: 10.14670/HH-11-973. PubMed PMID:29441509 .
  18. Annala, M, Vandekerkhove, G, Khalaf, D, Taavitsainen, S, Beja, K, Warner, EW et al.. Circulating Tumor DNA Genomics Correlate with Resistance to Abiraterone and Enzalutamide in Prostate Cancer. Cancer Discov. 2018;8 (4):444-457. doi: 10.1158/2159-8290.CD-17-0937. PubMed PMID:29367197 .
  19. Högnäs, G, Kivinummi, K, Kallio, HML, Hieta, R, Ruusuvuori, P, Koskenalho, A et al.. Feasibility of Prostate PAXgene Fixation for Molecular Research and Diagnostic Surgical Pathology: Comparison of Matched Fresh Frozen, FFPE, and PFPE Tissues. Am J Surg Pathol. 2018;42 (1):103-115. doi: 10.1097/PAS.0000000000000961. PubMed PMID:28984675 .
  20. Nättinen, J, Jylhä, A, Aapola, U, Enríquez-de-Salamanca, A, Pinto-Fraga, J, López-Miguel, A et al.. Topical fluorometholone treatment and desiccating stress change inflammatory protein expression in tears. Ocul Surf. 2018;16 (1):84-92. doi: 10.1016/j.jtos.2017.09.003. PubMed PMID:28918083 .

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