Publications 1994 2019

2019

Anagrelide for Gastrointestinal Stromal Tumor

Pulkka, O-P., Gebreyohannes, Y. K., Wozniak, A., Mpindi, J-P., Tynninen, O., Icay, K., Cervera, A., Keskitalo, S., Murumägi, A., Kulesskiy, E., Laaksonen, M., Wennerberg, K., Varjosalo, M., Laakkonen, P., Lehtonen, R., Hautaniemi, S., Kallioniemi, O., Schöffski, P., Sihto, H. & Joensuu, H., 1 Mar 2019, In : Clinical Cancer Research. 25, 5, p. 1676-1687 12 p.

Research output: Contribution to journalArticleScientificpeer-review

BRAF immunohistochemistry predicts sentinel lymph node involvement in intermediate thickness melanomas

Manninen, A. A., Gardberg, M., Juteau, S., Ilmonen, S., Jukonen, J., Andersson, N. & Carpen, O., 30 Apr 2019, In : PLoS One. 14, 4, 13 p., 0216043.

Research output: Contribution to journalArticleScientificpeer-review

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Breast cancer outcome prediction with tumour tissue images and machine learning

Turkki, R., Byckhov, D., Lundin, M., Isola, J., Nordling, S., Kovanen, P. E., Verrill, C., von Smitten, K., Joensuu, H., Lundin, J. & Linder, N., 22 May 2019, In : Breast Cancer Research and Treatment. 177, 1, p. 41-52 12 p.

Research output: Contribution to journalArticleScientificpeer-review

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Clinical features and outcome of the patients with sinonasal tract diffuse large B-cell lymphoma in the pre-rituximab and rituximab eras

Vähämurto, P., Mannisto, S., Pollari, M., Karjalainen-Lindsberg, M-L., Mäkitie, A. A. & Leppä, S., Jun 2019, In : European Journal of Haematology. 102, 6, p. 457-464 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Combined epithelial marker analysis of tumour budding in stage II colorectal cancer

Slik, K., Blom, S., Turkki, R., Välimäki, K., Kurki, S., Mustonen, H., Haglund, C., Carpén, O., Kallioniemi, O., Korkeila, E., Sundström, J. & Pellinen, T., Jan 2019, In : The Journal of Pathology: Clinical Research. 5, 1, p. 63-78 16 p.

Research output: Contribution to journalArticleScientificpeer-review

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Critical questions in ovarian cancer research and treatment: Report of an American Association for Cancer Research Special Conference

Bast, R. C., Matulonis, U. A., Sood, A. K., Ahmed, A. A., Amobi, A. E., Balkwill, F. R., Wielgos-Bonvallet, M., Bowtell, D. D. L., Brenton, J. D., Brugge, J. S., Coleman, R. L., Draetta, G. F., Doberstein, K., Drapkin, R. I., Eckert, M. A., Edwards, R. P., Elias, K. M., Ennis, D., Futreal, A., Gershenson, D. M. & 23 othersGreenberg, R. A., Huntsman, D. G., Ji, J. X. Y., Kohn, E. C., Iavarone, C., Lengyel, E. R., Levine, D. A., Lord, C. J., Lu, Z., Mills, G. B., Modugno, F., Nelson, B. H., Odunsi, K., Pilsworth, J. A., Rottapel, R. K., Powell, D. J., Shen, L., Shih, I-M., Spriggs, D. R., Walton, J., Zhang, K., Zhang, R. & Zou, L., 15 Jun 2019, In : Cancer. 125, 12, p. 1963-1972 10 p.

Research output: Contribution to journalEditorialScientificpeer-review

Deep learning for detecting tumour-infiltrating lymphocytes in testicular germ cell tumours

Linder, N., Taylor, J. C., Colling, R., Pell, R., Alveyn, E., Joseph, J., Protheroe, A., Lundin, M., Lundin, J. & Verrill, C., Feb 2019, In : Journal of Clinical Pathology. 72, 2, p. 157-164 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Detection of breast cancer lymph node metastases in frozen sections with a point-of care low-cost microscope scanner

Holmström, O., Linder, N., Moilanen, H., Suutala, A., Nordling, S., Ståhls, A., Lundin, M., Diwan, V. & Lundin, J., 19 Mar 2019, In : PLoS One. 14, 3, 15 p., 0208366.

Research output: Contribution to journalArticleScientificpeer-review

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Fibroblast as a critical stromal cell type determining prognosis in prostate cancer

Blom, S., Erickson, A., Östman, A., Rannikko, A., Mirtti, T., Kallioniemi, O. & Pellinen, T., 3 Jul 2019, In : Prostate. p. 1505-1513 9 p.

Research output: Contribution to journalArticleScientificpeer-review

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Impact of constitutional TET2 haploinsufficiency on molecular and clinical phenotype in humans

Kaasinen, E., Kuismin, O., Rajamäki, K., Ristolainen, H., Aavikko, M., Kondelin, J., Saarinen, S., Berta, D. G., Katainen, R., Hirvonen, E. A. M., Karhu, A., Taira, A., Tanskanen, T., Alkodsi, A., Taipale, M., Morgunova, E., Franssila, K., Lehtonen, R., Mäkinen, M., Aittomäki, K. & 15 othersPalotie, A., Kurki, M., Pietiläinen, O., Hilpert, M., Saarentaus, E., Niinimäki, J., Junttila, J., Kaikkonen, K., Vahteristo, P., Skoda, R. C., Seppänen, M. R. J., Eklund, K. K., Taipale, J., Kilpivaara, O. & Aaltonen, L. A., 19 Mar 2019, In : Nature Communications. 10, 17 p., 1252.

Research output: Contribution to journalArticleScientificpeer-review

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Lähtökohdaltaan tuntematon syöpä

Suonpää, P., Nevala, R., Beule, A., Schildt, J., Bova, S. & Mirtti, T., 2019, In : Duodecim. 135, 9, p. 838-846 9 p.

Research output: Contribution to journalReview ArticleScientificpeer-review

Making Sense of the Epigenome Using Data Integration Approaches

Cazaly, E., Saad, J., Wang, W., Heckman, C., Ollikainen, M. & Tang, J., 19 Feb 2019, In : Frontiers in Pharmacology. 10, 15 p., 126.

Research output: Contribution to journalReview ArticleScientificpeer-review

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Management of clinically N0 neck in oropharyngeal carcinoma

Jouhi, L., Atula, T., Mäkitie, A. & Keski-Santti, H., Apr 2019, In : European Archives of Oto-Rhino-Laryngology. 276, 4, p. 1205-1210 6 p.

Research output: Contribution to journalArticleScientificpeer-review

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Mathematical modeling of treatment resistance in cancer

Kozłowska, E., 2019, Helsinki: [E. Kozłowska]. 52 p.

Research output: ThesisDoctoral ThesisCollection of Articles

Open Access

Meiotic spindle assembly checkpoint and aneuploidy in males versus females

Lane, S. & Kauppi, L., Mar 2019, In : Cellular and Molecular Life Sciences. 76, 6, p. 1135-1150 16 p.

Research output: Contribution to journalReview ArticleScientificpeer-review

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Open Source Infrastructure for Health Care Data Integration and Machine Learning Analyses

Isoviita, V-M., Salminen, L., Azar, J., Lehtonen, R., Roering, P., Carpen, O. M., Hietanen, S., Grénman, S., Hynninen, J., Färkkilä, A. & Hautaniemi, S., 27 Aug 2019, In : JCO Clinical Cancer Informatics. 3, p. 1-16 16 p.

Research output: Contribution to journalArticleScientificpeer-review

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Performance of Finnish biobanks in nationwide pulmonary carcinoid tumour research

Vesterinen, T., Salmenkivi, K., Mustonen, H., Kuopio, T., Lappi-Blanco, E., Paavonen, T., Vainio, P., Knuuttila, A., Carpén, O., Haglund, C. & Arola, J., 5 Aug 2019, In : Virchows Archiv.

Research output: Contribution to journalArticleScientificpeer-review

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Prospective Longitudinal ctDNA Workflow Reveals Clinically Actionable Alterations in Ovarian Cancer

Oikkonen, J., Zhang, K., Salminen, L., Schulman, I., Lavikka, K., Andersson, N., Ojanperä, E., Hietanen, S., Grénman, S., Lehtonen, R., Huhtinen, K., Carpén, O., Hynninen, J., Färkkilä, A. & Hautaniemi, S., 3 May 2019, In : JCO Precision Oncology. 3, p. 1-12 12 p.

Research output: Contribution to journalArticleScientificpeer-review

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Suomalainen biopankki on potilaita varten

Carpén, O. & Hautalahti, M., 2019, In : Duodecim. 135, 10, p. 971-972 2 p.

Research output: Contribution to journalEditorialProfessional

The plasticity of mesenchymal stem cells in regulating surface HLA-I

Wang, Y., Huang, J., Gong, L., Yu, D., An, C., Bunpetch, V., Dai, J., Huang, H., Zou, X., Ouyang, H. & Liu, H., 11 Apr 2019, In : iScience.

Research output: Contribution to journalArticleScientificpeer-review

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Transcription Factor USF1 Is Required for Maintenance of Germline Stem Cells in Male Mice

Faisal, I., Cisneros-Montalvo, S., Hamer, G., Tuominen, M. M., Laurila, P-P., Tumiati, M., Jauhiainen, M., Kotaja, N., Toppari, J., Mäkelä, J-A. & Kauppi, L., May 2019, In : Endocrinology. 160, 5, p. 1119-1136 18 p.

Research output: Contribution to journalArticleScientificpeer-review

Using online game-based platforms to improve student performance and engagement in histology teaching

Felszeghy, S., Pasonen-Seppänen, S., Koskela, A., Nieminen, P., Härkönen, K., Paldanius, K. M. A., Gabbouj, S., Ketola, K., Hiltunen, M., Lundin, M., Haapaniemi, T., Sointu, E., Bauman, E. B., Gilbert, G. E., Morton, D. & Mahonen, A., 22 Jul 2019, In : BMC Medical Education. 19, 1

Research output: Contribution to journalArticleScientificpeer-review

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Vaginal Microbiota Composition Correlates Between Pap Smear Microscopy and Next Generation Sequencing and Associates to Socioeconomic Status

Virtanen, S., Rantsi, T., Virtanen, A., Kervinen, K., Nieminen, P., Kalliala, I. & Salonen, A., 23 May 2019, In : Scientific Reports. 9, 9 p., 7750.

Research output: Contribution to journalArticleScientificpeer-review

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Validation of IMPROD biparametric MRI in men with clinically suspected prostate cancer: A prospective multi-institutional trial

Jambor, I., Verho, J., Ettala, O., Knaapila, J., Taimen, P., Syvänen, K. T., Kiviniemi, A., Kähkönen, E., Perez, I. M., Seppänen, M., Rannikko, A., Oksanen, O., Riikonen, J., Vimpeli, S. M., Kauko, T., Merisaari, H., Kallajoki, M., Mirtti, T., Lamminen, T., Saunavaara, J. & 2 othersAronen, H. J. & Boström, P. J., 3 Jun 2019, In : PLoS Medicine. 16, 6, p. e1002813

Research output: Contribution to journalArticleScientificpeer-review

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2018

A Functional Homologous Recombination Assay Predicts Primary Chemotherapy Response and Long-Term Survival in Ovarian Cancer Patients

Tumiati, M., Hietanen, S., Hynninen, J., Pietilä, E., Färkkilä, A., Kaipio, K., Roering, P., Huhtinen, K., Alkodsi, A., Li, Y., Lehtonen, R., Erkan, E. P., Tuominen, M. M., Lehti, K., Hautaniemi, S. K., Vähärautio, A., Grenman, S., Carpen, O. & Kauppi, L., 15 Sep 2018, In : Clinical Cancer Research. 24, 18, p. 4482-4493 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Building a science communications platform: A recipe from The Science Basement

Facciotto, C. & Baibuz, E., 2018, In : Hindawi Blog.

Research output: Contribution to journalArticleGeneral public

Clinical Value of 18F-fluorodeoxyglucose Positron Emission Tomography/Computed Tomography in Response Evaluation after Primary Treatment of Advanced Epithelial Ovarian Cancer

Hynninen, J., Laasik, M., Vallius, T., Kemppainen, J., Grönroos, S., Virtanen, J., Casado, J., Hautaniemi, S., Grenman, S., Seppänen, M. & Auranen, A., Aug 2018, In : Clinical Oncology. 30, 8, p. 507-514 8 p.

Research output: Contribution to journalArticleScientificpeer-review

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Combined ASRGL1 and p53 immunohistochemistry as an independent predictor of survival in endometrioid endometrial carcinoma

Huvila, J., Laajala, T. D., Edqvist, P-H., Mardinoglu, A., Talve, L., Ponten, F., Grenman, S., Carpen, O., Aittokallio, T. & Auranen, A., Apr 2018, In : Gynecologic Oncology. 149, 1, p. 173-180 8 p.

Research output: Contribution to journalArticleScientificpeer-review

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Comprehensive evaluation of coding region point mutations in microsatellite-unstable colorectal cancer

Kondelin, J., Salokas, K., Saarinen, L., Ovaska, K., Rauanheimo, H., Plaketti, R-M., Hamberg, J., Liu, X., Yadav, L., Gylfe, A. E., Cajuso, T., Hänninen, U. A., Palin, K., Ristolainen, H., Katainen, R., Kaasinen, E., Tanskanen, T., Aavikko, M., Taipale, M., Taipale, J. & 17 othersRenkonen-Sinisalo, L., Lepistö, A., Koskensalo, S., Böhm, J., Mecklin, J-P., Ongen, H., Dermitzakis, E. T., Kilpivaara, O., Vahteristo, P., Turunen, M., Hautaniemi, S., Tuupanen, S., Karhu, A., Välimäki, N., Varjosalo, M., Pitkänen, E. & Aaltonen, L. A., 2018, In : EMBO molecular medicine. 10, 9, 20 p., e8552.

Research output: Contribution to journalArticleScientificpeer-review

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Computational analysis of microRNAs in biomedicine

Icay-Rouhiainen, K. A., 2018, Helsinki: [K. A. Icay-Rouhiainen]. 51 p.

Research output: ThesisDoctoral ThesisCollection of Articles

Computer vision for tissue characterization and outcome prediction in cancer

Turkki, R., 2018, Helsinki: Helsingin yliopisto. 66 p.

Research output: ThesisDoctoral ThesisCollection of Articles

Deep learning based tissue analysis predicts outcome in colorectal cancer

Bychkov, D., Linder, N., Turkki, R., Nordling, S., Kovanen, P. E., Verrill, C., Walliander, M., Lundin, M., Haglund, C. & Lundin, J., 21 Feb 2018, In : Scientific Reports. 8, 11 p., 3395.

Research output: Contribution to journalArticleScientificpeer-review

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EGFR gene copy number decreases during anti-EGFR antibody therapy in colorectal cancer

Birkman, E-M., Avoranta, T., Algars, A., Korkeila, E., Lintunen, M., Lahtinen, L., Kuopio, T., Ristamäki, R., Carpen, O. & Sundström, J., Dec 2018, In : Human Pathology. 82, p. 163-171 9 p.

Research output: Contribution to journalArticleScientificpeer-review

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Endometriumkarsinooman molekulaarinen luokittelu ja kudosperäiset ennustetekijät

Huvila, J. & Carpén, O., 2018, In : Duodecim. 134, 12, p. 1265-1271 7 p.

Research output: Contribution to journalReview ArticleScientificpeer-review

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Evolutionary history of metastatic breast cancer reveals minimal seeding from axillary lymph nodes

Ullah, I., Karthik, G-M., Alkodsi, A., Kjallquist, U., Stalhammar, G., Lovrot, J., Martinez, N-F., Lagergren, J., Hautaniemi, S., Hartman, J. & Bergh, J., 2 Apr 2018, In : Journal of Clinical Investigation. 128, 4, p. 1355-1370 16 p.

Research output: Contribution to journalArticleScientificpeer-review

Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)

Kjällquist, U., Erlandsson, R., Tobin, N. P., Alkodsi, A., Ullah, I., Stalhammar, G., Karlsson, E., Hatschek, T., Hartman, J., Linnarsson, S. & Bergh, J., 12 Feb 2018, In : BMC Cancer. 18, 17 p., 174.

Research output: Contribution to journalArticleScientificpeer-review

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Formin Proteins FHOD1 and INF2 in Triple-Negative Breast Cancer: Association With Basal Markers and Functional Activities

Heuser, V. D., Mansuri, N., Mogg, J., Kurki, S., Repo, H., Kronqvist, P., Carpen, O. & Gardberg, M., 24 Aug 2018, In : Breast cancer-Basic and clinical research. 12, 12 p., 1178223418792247.

Research output: Contribution to journalArticleScientificpeer-review

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Gastric cancer: immunohistochemical classification of molecular subtypes and their association with clinicopathological characteristics

Birkman, E-M., Mansuri, N., Kurki, S., Ålgars, A., Lintunen, M., Ristamäki, R., Sundström, J. & Carpen, O., Mar 2018, In : Virchows Archiv. 472, 3, p. 369-382 14 p.

Research output: Contribution to journalArticleScientificpeer-review

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Glycomic Profiling Highlights Increased Fucosylation in Pseudomyxoma Peritonei

Saarinen, L. A., Nummela, P., Leinonen, H., Heiskanen, A., Thiel, A., Haglund, C., Lepistö, A., Satomaa, T., Hautaniemi, S. & Ristimäki, A., 2 Aug 2018, In : Molecular & Cellular Proteomics. 17, 11, p. 2107-2118 12 p.

Research output: Contribution to journalArticleScientificpeer-review

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Identifying differentially methylated sites in samples with varying tumor purity

Häkkinen, A., Alkodsi, A., Facciotto, C., Zhang, K., Kaipio, K., Leppa, S., Carpen, O., Grenman, S., Hynninen, J., Hietanen, S., Lehtonen, R. & Hautaniemi, S., 15 Sep 2018, In : Bioinformatics. 34, 18, p. 3078-3085 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Increased HSF1 expression predicts shorter disease-specific survival of prostate cancer patients following radical prostatectomy

Björk, J. K., Ahonen, I., Mirtti, T., Erickson, A., Rannikko, A., Butzow, A., Nordling, S., Lundin, J., Lundin, M., Sistonen, L., Nees, M. & Akerfelt, M., 2018, In : Oncotarget. 9, 58, p. 31200-31213 14 p.

Research output: Contribution to journalArticleScientificpeer-review

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Integrated genome analysis of uterine leiomyosarcoma to identify novel driver genes and targetable pathways

Cuppens, T., Moisse, M., Depreeuw, J., Annibali, D., Colas, E., Gil-Moreno, A., Huvila, J., Carpen, O., Zikan, M., Matias-Guiu, X., Moerman, P., Croce, S., Lambrechts, D. & Amant, F., 15 Mar 2018, In : International Journal of Cancer. 142, 6, p. 1230-1243 14 p.

Research output: Contribution to journalArticleScientificpeer-review

ITGB1-dependent upregulation of Caveolin-1 switches TGF beta signalling from tumour-suppressive to oncogenic in prostate cancer

Pellinen, T., Blom, S., Sanchez, S., Välimäki, K., Mpindi, J-P., Azegrouz, H., Strippoli, R., Nieto, R., Viton, M., Palacios, I., Turkki, R., Wang, Y., Sanchez-Alvarez, M., Nordling, S., Bützow, A., Mirtti, T., Rannikko, A., Montoya, M. C., Kallioniemi, O. & del Pozo, M. A., 5 Feb 2018, In : Scientific Reports. 8, 1, 14 p., 2338.

Research output: Contribution to journalArticleScientificpeer-review

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Let-7 microRNA controls invasion-promoting lysosomal changes via the oncogenic transcription factor myeloid zinc finger-1

Tvingsholm, S. A., Hansen, M. B., Clemmensen, K. K. B., Brix, D. M., Rafn, B., Frankel, L. B., Louhimo, R., Moreira, J., Hautaniemi, S., Gromova, I., Jäättelä, M. & Kallunki, T., Feb 2018, In : Oncogenesis. 7, 15 p., 14.

Research output: Contribution to journalArticleScientificpeer-review

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Lymphatic endothelium stimulates melanoma metastasis and invasion via MMP14-dependent Notch3 and beta 1-integrin activation

Pekkonen, P., Alve, S., Balistreri, G., Gramolelli, S., Tatti-Bugaeva, O., Paatero, I., Niiranen, O., Tuohinto, K., Perala, N., Taiwo, A., Zinovkina, N., Repo, P., Icay, K., Ivaska, J., Saharinen, P., Hautaniemi, S., Lehti, K. & Ojala, P. M., 1 May 2018, In : eLife. 7, 28 p., 32490.

Research output: Contribution to journalArticleScientificpeer-review

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Mathematical Modeling Predicts Response to Chemotherapy and Drug Combinations in Ovarian Cancer

Kozlowska, E., Färkkilä, A., Vallius, T., Carpen, O., Kemppainen, J., Grenman, S., Lehtonen, R., Hynninen, J., Hietanen, S. & Hautaniemi, S., 15 Jul 2018, In : Cancer Research. 78, 14, p. 4036-4044 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Miten motivoida kansalaisia syöpäseulontoihin?

Nieminen, P. & Virtanen, A., 2018, In : Duodecim. 134, 23, p. 2397-2401 5 p.

Research output: Contribution to journalArticleProfessional