Publications

Auvinen Group: Epidemiology
Bova Group: PELICAN-Personalized Cancer Medicine
Emmert-Streib Group: Group Predictive Society and Data Analytics Lab
Granberg Group: Cancer Regulation and Immunology
Murtola Group: Pharmacoepidemiology and Chemoprevention
Nykter Group: Computational Biology
Ruusuvuori Group: Bioimage Informatics
Schleutker Group: Genetic Predisposition to Prostate Cancer
Tammela Group: Molecular Biology
Tolonen Group: Histopathology


Anssi Auvinen | Epidemiology

 

Pakarainen T, Nevalainen J, Talala K, Taari K, Raitanen J, Kujala P, Stenman UH, Tammela TLJ, Auvinen A. The number of screening cycles needed to reduce prostate cancer mortality in the Finnish section of the European Randomised Study of Screening for Prostate Cancer (ERSPC). Clin Cancer Res 2019;25:839-843

Lindberg A, Talala K, Kujala P, Stenman UH, Taari K, Kilpeläinen TP, Tammela TL, Auvinen A. Bias-corrected estimates of effects of PSA screening decisions on the risk of prostate cancer diagnosis and death. Int J Cancer 2019;145:632-638

Auvinen A, Rannikko A, Taari K, Kujala P, Mirtti T, Kenttämies A, Rinta-Kiikka I, Lehtimäki T, Oksala N, Pettersson K, Tammela TL. A randomized trial of early detection of clinically significant prostate cancer (ProScreen): study design and rationale. Eur J Epidemiol 2017;32:521-527

Pakarainen T, Raitanen J, Talala K, Taari K, Kujala P, Tammela T, Auvinen A. Number of screening rounds and post-screening prostate cancer incidence. Eur Urol 2016;70:499-505

Auvinen A, Moss, S, Tammela T, Taari K, Roobol M, Schröder FH, Bangma CH, Carlsson S, Aus G, Zappa M, Puliti D, Denis LJ, Nelen V, Kwiatkowski M, Randazzo M, Paez A, Lujan M, Hugosson J. Absolute effect of prostate cancer screening: Balance of benefits and harms by centre in the European Randomized Study of Prostate Cancer Screening. Clin Cancer Res 2016;22:243-249

Kilpeläinen T, Tammela TL, Malila N, Hakama M, Santti H, Määttänen L, Stenman UH, Kujala P, Auvinen A. The Finnish prostate cancer screening trial: Analyses on screening failures. Int J Cancer 2015;136:2437-43

Booth N, Rissanen P, Tammela TL, Määttänen L, Taari K, Auvinen A. Health-related quality of life in the Finnish trial of screening for prostate cancer. Eur Urol 2014;65:39-47

Schröder FH, Hugosson J, Roobol MJ, Tammela TLJ, Zappa M, Nelen V, Kwiatkowski M, Lujan M, Määttänen L, Lilja H, Denis LJ, Recker F, Paez A, Bangma CH, Carlsson S, Puliti D, Villers A, Rebillard X, Hakama M, Stenman UH, Kujala PM, Taari K, Van der Kwast T, van Schaik RH, de Koning HJ, Moss SM, Auvinen A. Screening and prostate cancer mortality: Results of the European Randomised Study of Screening for Prostate Cancer (ERSPC) at 13 years of follow-up. Lancet 2014;384:2027-35

Schröder FH, Hugosson J, Roobol MJ, Tammela TLJ, Ciatto S, Nelen V, Kwiatkowski M, Lujan M7, Lilja H, Zappa M, Denis LJ, Recker F, Páez A, Määttänen L, Bangma CH, Aus G, Carlsson S, Villers A, Rebillard X, Van der Kwast T, Kujala PM, Blijenberg BG, Stenman UH, Huber A, Taari K, Hakama M, Moss SM, de Koning HJ, Auvinen A. Prostate Cancer Mortality at 11 years of follow-up in the European Randomized study of Screening for Prostate Cancer (ERSPC). N Engl J Med 2012;366:981-990

Schröder FH, Hugosson J, Roobol MJ, Tammela TL, Ciatto S, Nelen V, Kwiatkowski M, Lujan M, Lilja H, Zappa M, Denis LJ, Recker F, Berenguer A, Määttänen L, Bangma CH, Aus G, Villers A, Rebillard X, van der Kwast T, Blijenberg BG, Moss SM, de Koning HJ, Auvinen A. Screening and prostate cancer mortality in a European randomized study. N Engl J Med 2009;360:1320-28

 

 


Steven Bova | PELICAN-Personalized Cancer Medicine

 

Google Scholar

Woodcock DJ, Riabchenko E, Taavitsainen S, Kankainen M, Gundem G, Brewer DS, Ellonen P, Lepistö M, Golubeva YG, Warner AC, Tolonen TT, Jasu J, Isaacs WB, Emmert-Buck MR, Nykter M, Visakorpi T, Bova GS, Wedge DC. Prostate cancer evolution from multilineage primary to single lineage metastasis in ten men with implications for liquid biopsy. Nat Commun. 2020 Oct 8;11(1):5070. PMID: 33033260.

ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature. 2020 Feb;578(7793):82-93.

Sainio M, Visakorpi T, Tolonen T, Ilvesaro J, Bova GS. Expression of neuroendocrine differentiation markers in lethal metastatic castration-resistant prostate cancer. Pathol Res Pract. 2018 Apr 26. pii: 0344-0338(18)30003-7.

Högnäs G, Kivinummi K, Kallio HML, Hieta R, Ruusuvuori P, Koskenalho A, Kesseli J, Tammela TLJ, Riikonen J, Ilvesaro J, Kares S, Hirvikoski PP, Laurila M, Mirtti T, Nykter M, Kujala PM, Visakorpi T, Tolonen T, Bova GS. 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 Jan;42(1):103-115.

Bova GS, Cancer Genomics: Human metastases under scrutiny. Nature, 2017 548(7667):287-288.

Behjati S, Gundem G, Wedge DC, Roberts ND, Tarpey PS, Cooke SL, Van Loo P, Alexandrov LB, Ramakrishna M, Davies H, Nik-Zainal S, Hardy C, Latimer C, Raine KM, Stebbings L, Menzies A, Jones D, Shepherd R, Butler AP, Teague JW, Jorgensen M, Khatri B, Pillay N, Shlien A, Futreal PA, Badie C; ICGC Prostate Group, McDermott U, Bova GS, Richardson AL, Flanagan AM, Stratton MR, Campbell PJ. Mutational signatures of ionizing radiation in second malignancies. Nat Commun. 2016 Sep 12;7:12605.

Bova GS, Kallio HML, Annala M, Kivinummi K, Högnäs G, Häyrynen S, Rantapero T, Kivinen V, Isaacs WB, Tolonen T, Nykter M, Visakorpi T. Integrated clinical, whole genome, and transcriptome analysis of multisampled lethal prostate cancer. Cold Spring Harbor Molecular Case Studies. 2016 May 2(3).

Gundem G, Van Loo P, Kremeyer B, Alexandrov LB, Tubio JMC, Papaemmanuil E, Brewer DS, Kallio HML, Högnäs G, Annala M, Kivinummi K, Goody V, Latimer C, O’Meara S, Dawson KJ, Isaacs W, Emmert-Buck MR, Nykter M, Foster C, Kote-Jarai Z, Easton D, Whitaker HC, Neal DE, Cooper CS,Eeles RA, Visakorpi T, Campbell PJ, McDermott U, Wedge DC, and Bova GS. The Evolutionary History of Lethal Metastatic Prostate Cancer. Nature, 520, 353-7, 2015.

Tubio JM, Li Y, Ju YS, Martincorena I, Cooke SL, Tojo M, Gundem G, Pipinikas CP, Zamora J, Raine K, Menzies A, Roman-Garcia P, Fullam A, Gerstung M, Shlien A, Tarpey PS, Papaemmanuil E, Knappskog S, Van Loo P, Ramakrishna M, Davies HR, Marshall J, Wedge DC, Teague JW, Butler AP, Nik-Zainal S, Alexandrov L, Behjati S, Yates LR, Bolli N, Mudie L, Hardy C, Martin S, McLaren S, O’Meara S, Anderson E, Maddison M, Gamble S; ICGC Breast Cancer Group; ICGC Bone Cancer Group; ICGC Prostate Cancer Group, Foster C, Warren AY, Whitaker H, Brewer D, Eeles R, Cooper C, Neal D, Lynch AG, Visakorpi T, Isaacs WB, van’t Veer L, Caldas C, Desmedt C, Sotiriou C, Aparicio S, Foekens JA, Eyfjörd JE, Lakhani SR, Thomas G, Myklebost O, Span PN, Børresen-Dale AL, Richardson AL, Van de Vijver M, Vincent-Salomon A, Van den Eynden GG, Flanagan AM, Futreal PA, Janes SM, Bova GS, Stratton MR, McDermott U, Campbell PJ. Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science. 2014 Aug 1;345(6196):1251343.

Liu W, Laitinen S, Khan S, Vihinen M, Kowalski J, Yu G, Chen L, Ewing CM, Eisenberger MA, Carducci MA, Nelson WG, Yegnasubramanian S, Luo J, Wang Y, Xu J, Isaacs WB, Visakorpi T, Bova GS. Copy Number Analysis Indicates Monoclonal Origin of Lethal Metastatic Prostate Cancer. Nature Medicine 2009; 15: 560-565.

 


Frank Emmert-Streib | Predictive Society and Data Analytics Lab

 

Azam, M., Musa, A., Dehmer, M., Yli-Harja, O. P., & Emmert-Streib, F. (2019). Global Genetics Research in Prostate Cancer: A Text Mining and Computational Network Theory Approach. Frontiers in genetics, 10, 70.

Moore, D., de Matos Simoes, R., Dehmer, M., & Emmert-Streib, F. (2019). Prostate cancer gene regulatory network inferred from RNA-Seq data. Current genomics, 20(1), 38-48.

Dehmer, M., Mueller, L. A., & Emmert-Streib, F. (2013). Quantitative network measures as biomarkers for classifying prostate cancer disease states: a systems approach to diagnostic biomarkers. PloS one, 8(11), e77602.

Emmert-Streib, F., Dehmer, M., & Haibe-Kains, B. (2014). Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks. Frontiers in cell and developmental biology, 2, 38.

Glazko, G. V., & Emmert-Streib, F. (2009). Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets. Bioinformatics, 25(18), 2348-2354.

Emmert-Streib, F., & Glazko, G. V. (2011). Pathway analysis of expression data: deciphering functional building blocks of complex diseases. PLoS Comput Biol, 7(5), e1002053.

Rahmatallah, Y., Emmert-Streib, F., & Glazko, G. (2014). Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets. Bioinformatics, 30(3), 360-368.

Olsen, C., Fleming, K., Prendergast, N., Rubio, R., Emmert-Streib, F., Bontempi, G., … & Quackenbush, J. (2014). Inference and validation of predictive gene networks from biomedical literature and gene expression data. Genomics, 103(5-6), 329-336.

Emmert-Streib, F., Tripathi, S., Simoes, R. D. M., Hawwa, A. F., & Dehmer, M. (2013). The human disease network: Opportunities for classification, diagnosis, and prediction of disorders and disease genes. Systems Biomedicine, 1(1), 20-28.

Tripathi, S., Dehmer, M., & Emmert-Streib, F. (2014). NetBioV: an R package for visualizing large network data in biology and medicine. Bioinformatics, 30(19), 2834-2836.


Kirsi Granberg | Cancer Regulation and Immunology

 

GoogleScholar

Dufva O, Pölönen P, Brück, O., Keränen, M, Klievink J, Mehtonen J, Huuhtanen J, Kumar A, Malani D, Siitonen S, Kankainen M, Ghimire B, Lahtela J, Mattila P, Vähä-Koskela M, Wennerberg K, Granberg K, Leivonen S-K, Meriranta L, Heckman C, Leppä S, Nykter M, Lohi O, Heinäniemi M, Mustjoki S. Immunogenomic landscape of hematological malignancies. Cancer Cell. In press.

Mehtonen J, Pölönen P, Häyrynen S, Dufva O, Lin J, Liuksiala T, Granberg K, Lohi O, Hautamäki V, Nykter M, Heinäniemi M. Data-driven characterization of molecular phenotypes across heterogeneous sample collections. Nucleic Acids Res. 2019 Jul 26;47(13):e76.

Luoto S, Hermelo I, Vuorinen E, Hannus P, Kesseli J, Nykter M, Granberg KJ. Computational characterization of suppressive immune microenvironments in glioblastoma. Cancer Res. 2018 Oct 1;78(19):5574-5585.

Nordfors K, Haapasalo J, Afyounian E, Tuominen J, Annala M, Häyrynen S, Karhu R, Helén P, Lohi O, Nykter M, Haapasalo H, Granberg KJ. 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 Apr 2;4(2):a002246.

Granberg KJ, Annala M, Lehtinen B, Kesseli J, Haapasalo J, Yli-Harja O, Visakorpi T, Haapasalo H, Nykter M, Zhang W. Strong FGFR3 staining is a marker for FGFR3 fusions in diffuse gliomas. Neuro Oncol. 2017 Sep 1;19(9):1206-1216.

Chua CY, Liu Y, Granberg KJ, Hu L, Haapasalo H, Annala M, Cogdell DE, Verploegen M, Moore LM, Fuller GN, Zhang W. IGFBP2 potentiates nuclear EGFR-STAT3 signaling. Oncogene. 2016 Feb 11; 35(6): 738–747.

Annala M, Kivinummi K, Tuominen J, Karakurt S, Granberg KJ, Latonen L, Ylipää A, Sjöblom L, Ruusuvuori P, Saramäki O, Kaukoniemi KM, Yli-Harja O, Vessella RL, Tammela TLJ, Zhang W, Visakorpi T, Nykter M. Recurrent SKIL-activating rearrangements in ETS-negative prostate cancer. Oncotarget. 2015 Mar 20; 6(8): 6235–6250.

Kong L, Aho K-L, Granberg KJ, Lund R, Järvenpää L, Seppälä J, Gokhale P, Leinonen K, Hahne L, Mäkelä J, Laurila K, Pukkila H, Nykter M, Andrews PW, Lahesmaa R, Yli-Harja O, Roos C, Autio, R. ESTOOLS Data@Hand, human stem cell gene expression resource. Nat Methods. 2013 Sep;10(9):814-5.

Parker BC, Annala MJ, Cogdell DE, Granberg, KJ, Sun Y, Ji P, Li X, Gumin J, Zheng H, Hu L, Yli-Harja O, Haapasalo H, Visakorpi T, Liu X, Liu CG, Sawaya R, Fuller GN, Chen K, Lang FF, Nykter M, Zhang W. The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma. J Clin Invest. 2013 Feb;123(2):855-65.

Rautajoki KJ, Marttila E, Nyman TA, Lahesmaa R. IL-4 inhibits Caspase-3 by regulating several proteins in the Fas pathway during initial stages of human Th2 cell differentiation. Mol Cell Proteomics. 2007 Feb;6(2):238-51.

 


Teemu Murtola | Pharmacoepidemiology and Chemoprevention

 

Raittinen P, Niemistö K, Pennanen E, Syvälä H, Auriola S, Riikonen J, Lehtimäki T, Ilmonen P, Murtola T. Circulatory and prostatic tissue lipidomic profiles shifts after high-dose atorvastatin use in men with prostate cancer. Sci Rep. 2020 Jul 21;10(1):12016.

Siltari A, Murtola TJ, Talala K, Taari K, Tammela TLJ, Auvinen A. Antihypertensive drug use and prostate cancer-specific mortality in Finnish men. PLoS One. 2020 Jun 29;15(6):e0234269.

Riikonen J, Pakarainen T, Siltari A, Pienimäki JP, Koskimäki J, Murtola TJ. Urine colour as an indicator for anastomotic leakage after robot-assisted radical prostatectomy. Scand J Urol. 2020

Siltari A, Riikonen J, Fode M, Murtola TJ. Effects of Preoperative Atorvastatin Treatment On Erectile Function After Radical Prostatectomy: Results From a Subgroup of ESTO1, a Randomized, Double-Blind, Placebo-Controlled Study. J Sex Med. 2019 Oct;16(10):1597-1605.

Joentausta RM, Murtola TJ. Prostate cancer survival among statin users after prostatectomy in a Finnish nationwide cohort. Prostate. 2019;79:583-591.

Knuuttila E, Riikonen J, Syvälä H, Auriola S, Murtola TJ. Access and concentrations of atorvastatin in the prostate in men with prostate cancer.  Prostate. 2019 Sep;79(12):1412-1419.

Murtola TJ, Veitonmäki T. Aspirin and Prostate Cancer Mortality: The Role of Tumor Grading Misclassification? Ann Intern Med. 2019 Apr 2;170(7):499-500.

Murtola TJ, Sälli SM, Talala K, Taari K, Tammela TLJ, Auvinen A. Blood glucose, glucose balance, and disease-specific survival after prostate cancer diagnosis in the Finnish Randomized Study of Screening for Prostate Cancer.  Prostate Cancer Prostatic Dis. 2019 Sep;22(3):453-460.

Santala EE, Rannikko A, Murtola TJ Antihypertensive drugs and prostate cancer survival after radical prostatectomy in Finland-A nationwide cohort study.  Int J Cancer. 2019 Feb 1;144(3):440-447.

Murtola TJ, Syvälä H, Tolonen T, Helminen M, Riikonen J, Koskimäki J, Pakarainen T, Kaipia A, Isotalo T, Kujala P, Tammela TL.  Atorvastatin Versus Placebo for Prostate Cancer Before Radical Prostatectomy-A Randomized, Double-blind, Placebo-controlled Clinical Trial.  J.Eur Urol. 2018 Dec;74(6):697-701.


Matti Nykter | Computational Biology

 

Google Scholar

Kohvakka A, Sattari M, Shcherban A, Annala M, Urbanucci A, Kesseli J, Tammela TLJ, Kivinummi K, Latonen L, Nykter M, Visakorpi T. AR and ERG drive the expression of prostate cancer specific long noncoding RNAs. Oncogene. 2020 Jul;39(30):5241-5251. doi: 10.1038/s41388-020-1365-6. Epub 2020 Jun 17. PMID: 32555329.

Dufva O, Pölönen P, Brück O, Keränen MAI, Klievink J, Mehtonen J, Huuhtanen J, Kumar A, Malani D, Siitonen S, Kankainen M, Ghimire B, Lahtela J, Mattila P, Vähä-Koskela M, Wennerberg K, Granberg K, Leivonen SK, Meriranta L, Heckman C, Leppä S, Nykter M, Lohi O, Heinäniemi M, Mustjoki S. Immunogenomic Landscape of Hematological Malignancies. Cancer Cell. 2020 Sep 14;38(3):380-399.e13. doi: 10.1016/j.ccell.2020.06.002. Epub 2020 Jul 9. Erratum in: Cancer Cell. 2020 Sep 14;38(3):424-428. PMID: 32649887.

Vandekerkhove G, Struss WJ, Annala M, Kallio HML, Khalaf D, Warner EW, Herberts C, Ritch E, Beja K, Loktionova Y, Hurtado-Coll A, Fazli L, So A, Black PC, Nykter M, Tammela T, Chi KN, Gleave ME, Wyatt AW. Circulating Tumor DNA Abundance and Potential Utility in De Novo Metastatic Prostate Cancer. Eur Urol. 2019 Apr;75(4):667-675. doi: 10.1016/j.eururo.2018.12.042. Epub 2019 Jan 10. PMID: 30638634.

Taavitsainen S, Annala M, Ledet E, Beja K, Miller PJ, Moses M, Nykter M, Chi KN, Sartor O, Wyatt AW. Evaluation of Commercial Circulating Tumor DNA Test in Metastatic Prostate Cancer. JCO Precis Oncol. 2019 Jun 12;3:PO.19.00014. doi: 10.1200/PO.19.00014. PMID: 32914020; PMCID: PMC7446428.

Pölönen P, Mehtonen J, Lin J, Liuksiala T, Häyrynen S, Teppo S, Mäkinen A, Kumar A, Malani D, Pohjolainen V, Porkka K, Heckman CA, May P, Hautamäki V, Granberg KJ, Lohi O, Nykter M, Heinäniemi M. Hemap: An Interactive Online Resource for Characterizing Molecular Phenotypes across Hematologic Malignancies. Cancer Res. 2019 May 15;79(10):2466-2479. doi: 10.1158/0008-5472.CAN-18-2970. Epub 2019 Apr 2. PMID: 30940663.

Mehtonen J, Pölönen P, Häyrynen S, Dufva O, Lin J, Liuksiala T, Granberg K, Lohi O, Hautamäki V, Nykter M, Heinäniemi M. Data-driven characterization of molecular phenotypes across heterogeneous sample collections. Nucleic Acids Res. 2019 Jul 26;47(13):e76. doi: 10.1093/nar/gkz281. PMID: 31329928; PMCID: PMC6648337.

Latonen L, Afyounian E, Jylhä A, Nättinen J, Aapola U, Annala M, Kivinummi KK, Tammela TTL, Beuerman RW, Uusitalo H, Nykter M, Visakorpi T. Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression. Nat Commun. 2018 Mar 21;9(1):1176. doi: 10.1038/s41467-018-03573-6. PMID: 29563510; PMCID: PMC5862881.

Annala M, Vandekerkhove G, Khalaf D, Taavitsainen S, Beja K, Warner EW, Sunderland K, Kollmannsberger C, Eigl BJ, Finch D, Oja CD, Vergidis J, Zulfiqar M, Azad AA, Nykter M, Gleave ME, Wyatt AW, Chi KN. Circulating Tumor DNA Genomics Correlate with Resistance to Abiraterone and Enzalutamide in Prostate Cancer. Cancer Discov. 2018 Apr;8(4):444-457. doi: 10.1158/2159-8290.CD-17-0937. Epub 2018 Jan 24. PMID: 29367197.

Annala M, Taavitsainen S, Vandekerkhove G, Bacon JVW, Beja K, Chi KN, Nykter M, Wyatt AW. Frequent mutation of the FOXA1 untranslated region in prostate cancer. Commun Biol. 2018 Aug 24;1:122. doi: 10.1038/s42003-018-0128-1. PMID: 30272002; PMCID: PMC6123809.

Gao Q, Liang WW, Foltz SM, Mutharasu G, Jayasinghe RG, Cao S, Liao WW, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ; Fusion Analysis Working Group; Cancer Genome Atlas Research Network, Chen K, Lazar AJ, Fields RC, Wendl MC, Van Tine BA, Vij R, Chen F, Nykter M, Shmulevich I, Ding L. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Rep. 2018 Apr 3;23(1):227-238.e3. doi: 10.1016/j.celrep.2018.03.050. PMID: 29617662; PMCID: PMC5916809.


Pekka Ruusuvuori | Bioimage Informatics

 

Valkonen, M., Högnäs, G., Bova, G.S., Ruusuvuori, P. Generalized fixation invariant nuclei detection through domain adaptation based deep learning, IEEE Journal of Biomedical and Health Informatics, 12 pages, in press, 2020

Ström, P., Kartasalo, K., Olsson, H., Solorzano, L., Delahunt, B., Berney, D. M., …Ruusuvuori, P. … & Eklund, M. (2020). Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study. The Lancet Oncology, 21(2), 222-232.

Valkonen, J. Isola, O. Ylinen, V. Muhonen, A. Saxlin, T. Tolonen, M. Nykter, P. Ruusuvuori. (2020). Cytokeratin-supervised deep learning for automatic recognition of epithelial cells in breast cancers stained for ER, PR, and Ki-67. IEEE Transactions on Medical Imaging, 39(2), 534-542.

Liimatainen, L. Kananen, L. Latonen, P. Ruusuvuori. Iterative unsupervised domain adaptation for generalized cell detection from brightfield z-stacks. BMC Bioinformatics, 20 (1), 80, 2019. 10.1186/s12859-019-2605-z

Kartasalo, L. Latonen.M. Vihinen, T. Visakorpi, M. Nykter, P. Ruusuvuori. Comparative analysis of tissue reconstruction algorithms for 3D histology. Bioinformatics, bty210, 2018

Ehteshami Bejnordi, M. Veta, PJ van Diest, B. van Ginneken, N. Karssemeijer, G. Litjens, JAWM van der Laak, The CAMELYON16 Consortium. Diagnostic assessment of deep learning algorithms for detection of lymph node metastases in women with breast cancer. JAMA 318 (22), 2199-2210

Valkonen, K. Kartasalo, K. Liimatainen, M. Nykter, L. Latonen, P. Ruusuvuori, Metastasis detection from whole slide images using local features and random forests. Cytometry A, 2017. doi:10.1002/cyto.a.23089

Valkonen, P. Ruusuvuori, K. Kartasalo, M. Nykter, T. Visakorpi, L. Latonen, Analysis of spatial heterogeneity in normal epithelium and preneoplastic alterations in mouse prostate tumor models. Scientific Reports, 2017. dx.doi.org/10.1038/srep44831

Ruusuvuori, L. Paavolainen, K. Rutanen, A. Mäki, H. Huttunen, V. Marjomäki. (2014) Quantitative Analysis of Dynamic Association in Live Biological Fluorescent Samples. PLoS ONE 9(4): e94245. doi:10.1371/journal.pone.0094245

Ruusuvuori, J. Lin, AC. Scott, Z. Tan, S. Sorsa, A. Kallio, M. Nykter, O. Yli-Harja, I. Shmulevich, AM. Dudley, Quantitative analysis of colony morphology in yeast, BioTechniques, Vol. 56, No. 1, Jan 2014, pp. 18–27.


Johanna Schleutker | Genetic Predisposition to Prostate Cancer

 

Google Scholar

Rantapero T, Wahlfors T, Kähler A, Hultman C, Lindberg J, Tammela TL, Nykter M, Schleutker J, Wiklund F. Inherited DNA Repair Gene Mutations in Men with Lethal Prostate Cancer. Genes (Basel), 2020,11(3):E314.

Chen SL, Fann JC, Sipeky C, Yang TK, Chiu SY, Yen AM, Laitinen V, Tammela TL, Stenman UH, Auvinen A, Schleutker J, Chen HH. Risk Prediction of Prostate Cancer with Single Nucleotide Polymorphisms (SNPs) and Prostate-Specific Antigen (PSA). J Urol, 2019; 201(3):486-495.

Kaikkonen E, Rantapero T, Zhang Q, Taimen P, Laitinen V, Kallajoki M, Jambulingam D, Ettala O, Knaapila J, Boström PJ, Wahlström G, Sipeky C, Pursiheimo J-P, Tammela T, Kellokumpu-Lehtinen P-L, PRACTICAL Consortium, Fey V, Maehle L, Wiklund F, Wei G-H, Schleutker J. ANO7 is associated with aggressive prostate cancer. Int J Cancer, 2018;143(10):2479-2487.

Sipeky C, Gao P, Zhang Q, Wang L, Ettala O, Talala KM, Tammela TLJ, Auvinen A, PRACTICAL Consortium, Wiklund F, Wei G-H, Schleutker J. Synergistic interaction of HOXB13 and CIP2A predispose to aggressive prostate cancer. Clin Cancer Res, 2018;24(24):6265-6276.

Chen Y, Zhang Q, Wang Q, Li J, Sipeky C, Xia J, Gao P, Hu Y, Zhang H, Yang X, Chen H, Jiang Y, Yang Y, Yao Z, Chen Y, Gao Y, Tan A, Liao M, Schleutker J, Xu J, Sun Y, Wei GH, Mo Z. Genetic association analysis of the RTK/ERK pathway with aggressive prostate cancer highlights the potential role of CCND2 in disease progression. Sci Rep, 2017; 7(1):4538.

Laitinen V, Rantapero T, Fischer D, Vuorinen EM, Tammela TLJ, PRACTICAL consortium, Wahlfors T, Schleutker J. Fine-mapping the 2q37 and 17q11.2-q22 loci for novel genes and sequence variants associated with a genetic predisposition to prostate cancer. Int J Cancer, 2015; 5;136(10):2316-2327..

Breyer JP, Bradley KM, Dorset DC, Clark TA, McReynolds K, Hock RL, Pereira JK, Maynard WH, Chang SS, Cookson MS, Smith JA, Schleutker J, Dupont WD, Smith JR. An expressed retrogene of master embryonic stem cell factor OCT4 alters prostate cancer susceptibility. Am J Hum Genet,2014; 6;94(3):395-404.

Chen LS, Fann JC, Chiu SY, Yen AM, Wahlfors T, Tammela TL, Chen HH, Auvinen A, Schleutker J. Assessing interactions of two loci (rs4242382 and rs10486567) in Familial Prostate Cancer: Statistical Evaluation of Epistasis. PLoS ONE, 2014; 9(2):e89508.

Cropp CD, Simpson CL, Wahlfors T, Ha N, George A, Jones MS, Harper U, Ponciano-Jackson D, Green TA, Tammela TL, Bailey-Wilson J, Schleutker J. Genome-wide linkage scan for prostate cancer susceptibility in Finland: Evidence for a novel locus on 2q37.2 and confirmation of signal on 17q21-q22. Int J Cancer, 2011; 129(10):2400-2407.

Nurminen R, Wahlfors T, Fischer D, Tammela TLJ, Schleutker J.  Identification of an aggressive prostate cancer predisposing variant at 11q13. Int J Cancer, 2011;129(3):599-606.


Teuvo Tammela | Molecular Biology

Fizazi K, Shore N, Tammela TL, Ulys A, Vjaters E, Polyakov S, Jievaltas M, Luz M, Alekseev B, Kuss I, Le Berre MA, Petrenciuc O, Snapir A, Sarapohja T, Smith MR; ARAMIS Investigators. Nonmetastatic, Castration-Resistant Prostate Cancer and Survival with Darolutamide. N Engl J Med. 2020 Sep 10;383(11):1040-1049.

Talala K, Heinävaara S, Taari K, Tammela TLJ, Kujala P, Stenman UH, Malila N, Auvinen A. Long-term health-related quality of life among men with prostate cancer in the Finnish randomized study of screening for prostate cancer. Cancer Med. 2020 Aug;9(15):5643-5654. doi: 10.1002/cam4.3181. Epub 2020 Jun 4.

Kohvakka A, Sattari M, Shcherban A, Annala M, Urbanucci A, Kesseli J, Tammela TLJ, Kivinummi K, Latonen L, Nykter M, Visakorpi T. AR and ERG drive the expression of prostate cancer specific long noncoding RNAs. Oncogene. 2020 Jul;39(30):5241-5251.

Booth N, Rissanen P, Tammela TLJ, Kujala P, Stenman UH, Taari K, Talala K, Auvinen A. Cost-effectiveness analysis of PSA-based mass screening: Evidence from a randomised controlled trial combined with register data. PLoS One. 2019 Nov 5;14(11):e0224479.

Assel M, Sjöblom L, Murtola TJ, Talala K, Kujala P, Stenman UH, Taari K, Auvinen A, Vickers A, Visakorpi T, Tammela TL, Lilja H. A Four-kallikrein Panel and β-Microseminoprotein in Predicting High-grade Prostate Cancer on Biopsy: An Independent Replication from the Finnish Section of the European Randomized Study of Screening for Prostate Cancer. Eur Urol Focus. 2019 Jul;5(4):561-567.

Na R, Helfand BT, Chen H, Conran CA, Crawford SE, Hayward SW, Tammela TLJ, Hoffman-Bolton J, Zheng SL, Walsh PC, Schleutker J, Platz EA, Isaacs WB, Xu J. A genetic variant near GATA3 implicated in inherited susceptibility and etiology of benign prostatic hyperplasia (BPH) and lower urinary tract symptoms (LUTS). Prostate. 2017 Aug;77(11):1213-1220.

Assel M, Sjöblom L, Murtola TJ, Talala K, Kujala P, Stenman UH, Taari K, Auvinen A, Vickers A, Visakorpi T, Tammela TL, Lilja H. A Four-kallikrein Panel and β-Microseminoprotein in Predicting High-grade Prostate Cancer on Biopsy: An Independent Replication from the Finnish Section of the European Randomized Study of Screening for Prostate Cancer. Eur Urol Focus. 2019 Jul;5(4):561-567.

Gusev A, Shi H, Kichaev G, Pomerantz M, Li F, Long HW, Ingles SA, Kittles RA, Strom SS, Rybicki BA, Nemesure B, Isaacs WB, Zheng W, Pettaway CA, Yeboah ED, Tettey Y, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Chokkalingam AP, John EM, Murphy AB, Signorello LB, Carpten J, Leske MC, Wu SY, Hennis AJ, Neslund-Dudas C, Hsing AW, Chu L, Goodman PJ, Klein EA, Witte JS, Casey G, Kaggwa S, Cook MB, Stram DO, Blot WJ, Eeles RA, Easton D, Kote-Jarai Z, Al Olama AA, Benlloch S, Muir K, Giles GG, Southey MC, Fitzgerald LM, Latonen L, Afyounian E, Jylhä A, Nättinen J, Aapola U, Annala M, Kivinummi KK, Tammela TTL, Beuerman RW, Uusitalo H, Nykter M, Visakorpi T. Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression. Nat Commun. 2018 Mar 21;9(1):1176.

Gronberg H, Wiklund F, Aly M, Henderson BE, Schleutker J, Wahlfors T, Tammela TL, Nordestgaard BG, Key TJ, Travis RC, Neal DE, Donovan JL, Hamdy FC, Pharoah P, Pashayan N, Khaw KT, Stanford JL, Thibodeau SN, McDonnell SK, Schaid DJ, Maier C, Vogel W, Luedeke M, Herkommer K, Kibel AS, Cybulski C, Wokolorczyk D, Kluzniak W, Cannon-Albright L, Teerlink C, Brenner H, Dieffenbach AK, Arndt V, Park JY, Sellers TA, Lin HY, Slavov C, Kaneva R, Mitev V, Batra J, Spurdle A, Clements JA, Teixeira MR, Pandha H, Michael A, Paulo P, Maia S, Kierzek A; PRACTICAL consortium, Conti DV, Albanes D, Berg C, Berndt SI, Campa D, Crawford ED, Diver WR, Gapstur SM, Gaziano JM, Giovannucci E, Hoover R, Hunter DJ, Johansson M, Kraft P, Le Marchand L, Lindström S, Navarro C, Overvad K, Riboli E, Siddiq A, Stevens VL, Trichopoulos D, Vineis P, Yeager M, Trynka G, Raychaudhuri S, Schumacher FR, Price AL, Freedman ML, Haiman CA, Pasaniuc B. Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation. Nat Commun. 2016 Apr 7;7:10979.

Ylipää A, Kivinummi K, Kohvakka A, Annala M, Latonen L, Scaravilli M, Kartasalo K, Leppänen SP, Karakurt S, Seppälä J, Yli-Harja O, Tammela TL, Zhang W, Visakorpi T, Nykter M. Transcriptome Sequencing Reveals PCAT5 as a Novel ERG-Regulated Long Noncoding RNA in Prostate Cancer. Cancer Res. 2015 Oct 1;75(19):4026-31.


Teemu Tolonen | Histopathology

 

Woodcock DJ, Riabchenko E, Taavitsainen S, Kankainen M, Gundem G, Brewer DS, Ellonen P, Lepistö M, Golubeva YG, Warner AC, Tolonen TT, Jasu J, Isaacs WB, Emmert-Buck MR, Nykter M, Visakorpi T, Bova GS, Wedge DC. Prostate cancer evolution from multilineage primary to single lineage metastasis in ten men with implications for liquid biopsy. Nat Commun. 2020 Oct 8;11(1):5070.

Sainio M, Visakorpi T, Tolonen T, Ilvesaro J, Bova GS. Expression of neuroendocrine differentiation markers in lethal metastatic castration-resistant prostate cancer. Pathol Res Pract. 2018 Apr 26. pii: 0344-0338(18)30003-7.

Högnäs G, Kivinummi K, Kallio HML, Hieta R, Ruusuvuori P, Koskenalho A, Kesseli J, Tammela TLJ, Riikonen J, Ilvesaro J, Kares S, Hirvikoski PP, Laurila M, Mirtti T, Nykter M, Kujala PM, Visakorpi T, Tolonen T, Bova GS. 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 Jan;42(1):103-115.

Tolonen TT, Tammela TL, Kujala PM, Tuominen VJ, Isola JJ, Visakorpi T. Histopathological variables and biomarkers enhancer of zeste homologue 2, Ki-67 and minichromosome maintenance protein 7 as prognosticators in primarily endocrine-treated prostate cancer. BJU Int. 2011;108:1430-1438.

Tolonen TT, Kujala PM, Laurila M, Tirkkonen M, Ilvesaro J, Tuominen VJ, Tammela TL, Isola J. Routine dual-color immunostaining with a 3-antibody cocktail improves the detection of small cancers in prostate needle biopsies. Hum Pathol. 2011;42:1635-1642.

Koivusalo L, Kaipia A, Kujala P, Isola J, Tolonen TT. Digital image analysis of the tissue surface areas of site-designated and bilaterally pooled prostate biopsies. Histol Histopathol 2018;33:399-405.

Tolonen T, Riikonen J, Tammela TLJ, Koivusalo L, Haapasalo H, Kujala P, Kaipia A. Extraprostatic extension in prostate biopsies is an under-recognized feature indicating high risk disease. Ann Diag Pathol 2018. doi: 10.1016/j.anndiagpath.2018.06.001

Tolonen TT, Kujala PM, Tammela TL, Tuominen VJ, Isola JJ, Visakorpi T. Overall and worst gleason scores are equally good predictors of prostate cancer progression. BMC Urol. 2011;11:21.

Näpänkangas, J., & Tolonen, T. Adoption of diagnostic digital pathology in Finland. Finnish Journal of EHealth and EWelfare. 2019:11;320–325.