Publications 2020

  1. Woodcock, DJ, Riabchenko, E, Taavitsainen, S, Kankainen, M, Gundem, G, Brewer, DS et al.. Prostate cancer evolution from multilineage primary to single lineage metastases with implications for liquid biopsy. Nat Commun. 2020;11 (1):5070. doi: 10.1038/s41467-020-18843-5. PubMed PMID:33033260 PubMed Central PMC7545111.
  2. Dufva, O, Pölönen, P, Brück, O, Keränen, MAI, Klievink, J, Mehtonen, J et al.. Immunogenomic Landscape of Hematological Malignancies. Cancer Cell. 2020;38 (3):424-428. doi: 10.1016/j.ccell.2020.08.019. PubMed PMID:32931743 .
  3. Gundem, G, Van Loo, P, Kremeyer, B, Alexandrov, LB, Tubio, JMC, Papaemmanuil, E et al.. Author Correction: The evolutionary history of lethal metastatic prostate cancer. Nature. 2020;584 (7820):E18. doi: 10.1038/s41586-020-2581-5. PubMed PMID:32728210 .
  4. Yang, M, Petralia, F, Li, Z, Li, H, Ma, W, Song, X et al.. Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics. Cell Syst. 2020;11 (2):186-195.e9. doi: 10.1016/j.cels.2020.06.013. PubMed PMID:32710834 .
  5. Dufva, O, Pölönen, P, Brück, O, Keränen, MAI, Klievink, J, Mehtonen, J et al.. Immunogenomic Landscape of Hematological Malignancies. Cancer Cell. 2020;38 (3):380-399.e13. doi: 10.1016/j.ccell.2020.06.002. PubMed PMID:32649887 .
  6. Khalaf, DJ, Aragón, IM, Annala, M, Lozano, R, Taavitsainen, S, Lorente, D et al.. HSD3B1 (1245A>C) germline variant and clinical outcomes in metastatic castration-resistant prostate cancer patients treated with abiraterone and enzalutamide: results from two prospective studies. Ann Oncol. 2020;31 (9):1186-1197. doi: 10.1016/j.annonc.2020.06.006. PubMed PMID:32574722 .
  7. Kohvakka, A, Sattari, M, Shcherban, A, Annala, M, Urbanucci, A, Kesseli, J et al.. AR and ERG drive the expression of prostate cancer specific long noncoding RNAs. Oncogene. 2020;39 (30):5241-5251. doi: 10.1038/s41388-020-1365-6. PubMed PMID:32555329 .
  8. Herberts, C, Murtha, AJ, Fu, S, Wang, G, Schönlau, E, Xue, H et al.. Activating AKT1 and PIK3CA Mutations in Metastatic Castration-Resistant Prostate Cancer. Eur Urol. 2020; :. doi: 10.1016/j.eururo.2020.04.058. PubMed PMID:32451180 .
  9. Tanjore Ramanathan, J, Lehtipuro, S, Sihto, H, Tóvári, J, Reiniger, L, Téglási, V et al.. Prostate-specific membrane antigen expression in the vasculature of primary lung carcinomas associates with faster metastatic dissemination to the brain. J Cell Mol Med. 2020;24 (12):6916-6927. doi: 10.1111/jcmm.15350. PubMed PMID:32390293 PubMed Central PMC7299712.
  10. Rantapero, T, Wahlfors, T, Kähler, A, Hultman, C, Lindberg, J, Tammela, TL et al.. Inherited DNA Repair Gene Mutations in Men with Lethal Prostate Cancer. Genes (Basel). 2020;11 (3):. doi: 10.3390/genes11030314. PubMed PMID:32183364 PubMed Central PMC7140841.
  11. Bacon, JVW, Annala, M, Soleimani, M, Lavoie, JM, So, A, Gleave, ME et al.. Plasma Circulating Tumor DNA and Clonal Hematopoiesis in Metastatic Renal Cell Carcinoma. Clin Genitourin Cancer. 2020;18 (4):322-331.e2. doi: 10.1016/j.clgc.2019.12.018. PubMed PMID:32046920 .
  12. Lindfors, K, Lin, J, Lee, HS, Hyöty, H, Nykter, M, Kurppa, K et al.. Metagenomics of the faecal virome indicate a cumulative effect of enterovirus and gluten amount on the risk of coeliac disease autoimmunity in genetically at risk children: the TEDDY study. Gut. 2020;69 (8):1416-1422. doi: 10.1136/gutjnl-2019-319809. PubMed PMID:31744911 PubMed Central PMC7234892.
  13. Ritch, E, Fu, SYF, Herberts, C, Wang, G, Warner, EW, Schönlau, E et al.. Identification of Hypermutation and Defective Mismatch Repair in ctDNA from Metastatic Prostate Cancer. Clin Cancer Res. 2020;26 (5):1114-1125. doi: 10.1158/1078-0432.CCR-19-1623. PubMed PMID:31744831 .
  14. Granberg, KJ, Raita, A, Lehtinen, B, Tiihonen, AM, Kesseli, J, Annala, M et al.. Moderate-to-strong expression of FGFR3 and TP53 alterations in a subpopulation of choroid plexus tumors. Histol Histopathol. 2020;35 (7):673-680. doi: 10.14670/HH-18-180. PubMed PMID:31660579 .
  15. Harjula, SE, Saralahti, AK, Ojanen, MJT, Rantapero, T, Uusi-Mäkelä, MIE, Nykter, M et al.. Characterization of immune response against Mycobacterium marinum infection in the main hematopoietic organ of adult zebrafish (Danio rerio). Dev Comp Immunol. 2020;103 :103523. doi: 10.1016/j.dci.2019.103523. PubMed PMID:31626817 .
  16. Valkonen, M, Isola, J, Ylinen, O, Muhonen, V, Saxlin, A, Tolonen, T et al.. Cytokeratin-Supervised Deep Learning for Automatic Recognition of Epithelial Cells in Breast Cancers Stained for ER, PR, and Ki-67. IEEE Trans Med Imaging. 2020;39 (2):534-542. doi: 10.1109/TMI.2019.2933656. PubMed PMID:31398111 .
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Publications 2019

  1. Jayaram, A, Wingate, A, Wetterskog, D, Conteduca, V, Khalaf, D, Sharabiani, MTA et al.. Plasma Androgen Receptor Copy Number Status at Emergence of Metastatic Castration-Resistant Prostate Cancer: A Pooled Multicohort Analysis. JCO Precis Oncol. 2019;3 :. doi: 10.1200/PO.19.00123. PubMed PMID:32923850 PubMed Central PMC7446348.
  2. Lindfors, K, Lin, J, Lee, HS, Hyöty, H, Nykter, M, Kurppa, K et al.. Metagenomics of the faecal virome indicate a cumulative effect of enterovirus and gluten amount on the risk of coeliac disease autoimmunity in genetically at risk children: the TEDDY study. Gut. 2020;69 (8):1416-1422. doi: 10.1136/gutjnl-2019-319809. PubMed PMID:31744911 PubMed Central PMC7234892.
  3. Ritch, E, Fu, SYF, Herberts, C, Wang, G, Warner, EW, Schönlau, E et al.. Identification of Hypermutation and Defective Mismatch Repair in ctDNA from Metastatic Prostate Cancer. Clin Cancer Res. 2020;26 (5):1114-1125. doi: 10.1158/1078-0432.CCR-19-1623. PubMed PMID:31744831 .
  4. Khalaf, DJ, Annala, M, Taavitsainen, S, Finch, DL, Oja, C, Vergidis, J et al.. Optimal sequencing of enzalutamide and abiraterone acetate plus prednisone in metastatic castration-resistant prostate cancer: a multicentre, randomised, open-label, phase 2, crossover trial. Lancet Oncol. 2019;20 (12):1730-1739. doi: 10.1016/S1470-2045(19)30688-6. PubMed PMID:31727538 .
  5. Granberg, KJ, Raita, A, Lehtinen, B, Tiihonen, AM, Kesseli, J, Annala, M et al.. Moderate-to-strong expression of FGFR3 and TP53 alterations in a subpopulation of choroid plexus tumors. Histol Histopathol. 2020;35 (7):673-680. doi: 10.14670/HH-18-180. PubMed PMID:31660579 .
  6. Harjula, SE, Saralahti, AK, Ojanen, MJT, Rantapero, T, Uusi-Mäkelä, MIE, Nykter, M et al.. Characterization of immune response against Mycobacterium marinum infection in the main hematopoietic organ of adult zebrafish (Danio rerio). Dev Comp Immunol. 2020;103 :103523. doi: 10.1016/j.dci.2019.103523. PubMed PMID:31626817 .
  7. Genitsch, V, Kollár, A, Vandekerkhove, G, Blarer, J, Furrer, M, Annala, M et al.. Morphologic and genomic characterization of urothelial to sarcomatoid transition in muscle-invasive bladder cancer. Urol Oncol. 2019;37 (11):826-836. doi: 10.1016/j.urolonc.2019.09.025. PubMed PMID:31585777 .
  8. Moradi, E, Marttinen, M, Häkkinen, T, Hiltunen, M, Nykter, M. Supervised pathway analysis of blood gene expression profiles in Alzheimer's disease. Neurobiol Aging. 2019;84 :98-108. doi: 10.1016/j.neurobiolaging.2019.07.004. PubMed PMID:31522136 .
  9. Pölönen, P, Jawahar Deen, A, Leinonen, HM, Jyrkkänen, HK, Kuosmanen, S, Mononen, M et al.. Nrf2 and SQSTM1/p62 jointly contribute to mesenchymal transition and invasion in glioblastoma. Oncogene. 2019;38 (50):7473-7490. doi: 10.1038/s41388-019-0956-6. PubMed PMID:31444413 .
  10. Valkonen, M, Isola, J, Ylinen, O, Muhonen, V, Saxlin, A, Tolonen, T et al.. Cytokeratin-Supervised Deep Learning for Automatic Recognition of Epithelial Cells in Breast Cancers Stained for ER, PR, and Ki-67. IEEE Trans Med Imaging. 2020;39 (2):534-542. doi: 10.1109/TMI.2019.2933656. PubMed PMID:31398111 .
  11. Genitsch, V, Kollár, A, Vandekerkhove, G, Blarer, J, Furrer, M, Annala, M et al.. Morphologic and genomic characterization of urothelial to sarcomatoid transition in muscle-invasive bladder cancer. Urol Oncol. 2019;37 (9):573.e19-573.e29. doi: 10.1016/j.urolonc.2019.06.021. PubMed PMID:31358384 .
  12. Mehtonen, J, Pölönen, P, Häyrynen, S, Dufva, O, Lin, J, Liuksiala, T et al.. Data-driven characterization of molecular phenotypes across heterogeneous sample collections. Nucleic Acids Res. 2019;47 (13):e76. doi: 10.1093/nar/gkz281. PubMed PMID:31329928 PubMed Central PMC6648337.
  13. Taavitsainen, S, Annala, M, Ledet, E, Beja, K, Miller, PJ, Moses, M et al.. Evaluation of Commercial Circulating Tumor DNA Test in Metastatic Prostate Cancer. JCO Precis Oncol. 2019;3 :. doi: 10.1200/PO.19.00014. PubMed PMID:32914020 PubMed Central PMC7446428.
  14. Yang, J, Ylipää, A, Sun, Y, Zheng, H, Chen, K, Nykter, M et al.. Editor's Note: Genomic and Molecular Characterization of Malignant Peripheral Nerve Sheath Tumor Identifies the IGF1R Pathway as a Primary Target for Treatment. Clin Cancer Res. 2019;25 (10):3195. doi: 10.1158/1078-0432.CCR-19-1144. PubMed PMID:31092619 .
  15. Hotte, SJ, Chi, KN, Joshua, AM, Tu, D, Macfarlane, RJ, Gregg, RW et al.. A Phase II Study of PX-866 in Patients With Recurrent or Metastatic Castration-resistant Prostate Cancer: Canadian Cancer Trials Group Study IND205. Clin Genitourin Cancer. 2019;17 (3):201-208.e1. doi: 10.1016/j.clgc.2019.03.005. PubMed PMID:31056399 .
  16. Pölönen, P, Mehtonen, J, Lin, J, Liuksiala, T, Häyrynen, S, Teppo, S et al.. Hemap: An Interactive Online Resource for Characterizing Molecular Phenotypes across Hematologic Malignancies. Cancer Res. 2019;79 (10):2466-2479. doi: 10.1158/0008-5472.CAN-18-2970. PubMed PMID:30940663 .
  17. Lehtipuro, S, Nykter, M, Granberg, KJ. Modes of immunosuppression in glioblastoma microenvironment. Oncotarget. 2019;10 (9):920-921. doi: 10.18632/oncotarget.26643. PubMed PMID:30847018 PubMed Central PMC6398170.
  18. Viiri, LE, Rantapero, T, Kiamehr, M, Alexanova, A, Oittinen, M, Viiri, K et al.. Extensive reprogramming of the nascent transcriptome during iPSC to hepatocyte differentiation. Sci Rep. 2019;9 (1):3562. doi: 10.1038/s41598-019-39215-0. PubMed PMID:30837492 PubMed Central PMC6401154.
  19. Sundahl, N, Vandekerkhove, G, Decaestecker, K, Meireson, A, De Visschere, P, Fonteyne, V et al.. Randomized Phase 1 Trial of Pembrolizumab with Sequential Versus Concomitant Stereotactic Body Radiotherapy in Metastatic Urothelial Carcinoma. Eur Urol. 2019;75 (5):707-711. doi: 10.1016/j.eururo.2019.01.009. PubMed PMID:30665814 .
  20. Vandekerkhove, G, Struss, WJ, Annala, M, Kallio, HML, Khalaf, D, Warner, EW et al.. Circulating Tumor DNA Abundance and Potential Utility in De Novo Metastatic Prostate Cancer. Eur Urol. 2019;75 (4):667-675. doi: 10.1016/j.eururo.2018.12.042. PubMed PMID:30638634 .
  21. Gubina, N, Naudi, A, Stefanatos, R, Jove, M, Scialo, F, Fernandez-Ayala, DJ et al.. Essential Physiological Differences Characterize Short- and Long-Lived Strains of Drosophila melanogaster. J Gerontol A Biol Sci Med Sci. 2019;74 (12):1835-1843. doi: 10.1093/gerona/gly143. PubMed PMID:29945183 .
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Publications 2018

  1. Annala, M, Taavitsainen, S, Vandekerkhove, G, Bacon, JVW, Beja, K, Chi, KN et al.. Frequent mutation of the FOXA1 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 TP53 and ATRX 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 TP53 and ATRX 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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Earlier publications

For complete publications list see here.

Disclaimer: Above publications lists are automatically generated from pubmed. Thus, they may not be exhaustive and may contain publications not related to Computational Biology group.