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Publications 2012 2019

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

Open Access
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Immune cell constitution in bone marrow microenvironment predicts outcome in adult ALL

Hohtari, H., Bruck, O., Blom, S., Turkki, R., Sinisalo, M., Kovanen, P. E., Kallioniemi, O., Pellinen, T., Porkka, K. & Mustjoki, S., Jul 2019, In : Leukemia. 33, 7, p. 1570-1582 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2018

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

Open Access
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Immune cell contexture in the bone marrow tumor microenvironment impacts therapy response in CML

Bruck, O., Blom, S., Dufva, O., Turkki, R., Chheda, H., Ribeiro, A., Kovanen, P., Aittokallio, T., Koskenvesa, P., Kallioniemi, O., Porkka, K., Pellinen, T. & Mustjoki, S., Jul 2018, In : Leukemia. 32, 7, p. 1643-1656 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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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

Open Access
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Spatial aspects of oncogenic signalling determine the response to combination therapy in slice explants from Kras-driven lung tumours

Närhi, K., Nagaraj, A. S., Parri, E., Turkki, R., van Duijn, P. W., Hemmes, A., Lahtela, J., Uotinen, V., Mäyränpää, M. I., Salmenkivi, K., Räsänen, J., Linder, N., Trapman, J., Rannikko, A., Kallioniemi, O., Af Hällström, T. M., Lundin, J., Sommergruber, W., Anders, S. & Verschuren, E. W., May 2018, In : Journal of Pathology. 245, 1, p. 101-113 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
2017

Exploration of tissue morphologies in breast cancer samples using unsupervised machine learning

Turkki, R., Bychkov, D., Linder, N., Isola, J., Joensuu, H. T. & Lundin, J., 1 Jul 2017, In : Cancer Research. 77, 13 Supplement, p. 673 1 p.

Research output: Contribution to journalMeeting AbstractResearchpeer-review

High Amount of PD1+TIM3+ T Helper Cells May Predict Poor Outcome in Adult Acute Lymphoblastic Leukemia

Hohtari, H., Bruck, O., Blom, S., Turkki, R., Ribeiro, A., Sinisalo, M., Kovanen, P., Kallioniemi, O., Pellinen, T., Porkka, K. & Mustjoki, S., 2017, p. 3985. 1 p.

Research output: Conference materialsAbstractResearchpeer-review

IMMUNOLOGICAL CHARACTERIZATION OF PH plus ALL BONE MARROW BY MULTIPLEX IMMUNOHISTOCHEMISTRY

Hohtari, H., Bruck, O., Blom, S., Turkki, R., Ribeiro, A., Sinisalo, M., Kovanen, P., Kallioniemi, O., Pellinen, T., Porkka, K. & Mustjoki, S., 26 Jun 2017, In : Haematologica. 102, p. 654-654 1 p.

Research output: Contribution to journalMeeting AbstractResearchpeer-review

Open Access
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Systems pathology by multiplexed immunohistochemistry and whole-slide digital image analysis

Blom, S., Paavolainen, L., Bychkov, D., Turkki, R., Maki-Teeri, P., Hemmes, A., Valimaki, K., Lundin, J., Kallioniemi, O. & Pellinen, T., 14 Nov 2017, In : Scientific Reports. 7, 13 p., 15580.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Chronic Activation of Innate Immunity Correlates With Poor Prognosis in Cancer Patients Treated With Oncolytic Adenovirus

Taipale, K., Liikanen, I., Juhila, J., Turkki, R., Tahtinen, S., Kankainen, M., Vassilev, L., Ristimaki, A., Koski, A., Kanerva, A., Diaconu, I., Cerullo, V., Vaha-Koskela, M., Oksanen, M., Linder, N., Joensuu, T., Lundin, J. & Hemminki, A., Jan 2016, In : Molecular therapy. 24, 1, p. 175-183 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

Deep learning for tissue microarray image-based outcome prediction in patients with colorectal cancer

Bychkov, D., Turkki, R., Haglund, C., Linder, N. & Lundin, J., 2016, Medical Imaging 2016: Digital Pathology. Gurcan, M. N. & Madabhushi, A. (eds.). SPIE - INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING, p. 979115 6 p. (Proceedings of SPIE; vol. 9791).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Identification of immune cell infiltration in hematoxylin-eosin stained breast cancer samples: Texture-based classification of tissue morphologies

Turkki, R., Linder, N., Kovanen, P. E., Pellinen, T. & Lundin, J., 2016, MEDICAL IMAGING 2016: DIGITAL PATHOLOGY. Gurcan, MN. & Madabhushi, A. (eds.). SPIE - INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING, 7 p. 979110. (Proceedings of SPIE; vol. 9791).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Immune cell profiling in CML bone marrow by multiplex IHC

Bruck, O., Blom, S., Turkki, R., Kovanen, P., Ribeiro, A., Linder, N., Lundin, J., Kallioniemi, O., Pellinen, T. & Mustjoki, S., Nov 2016, In : Annals of Oncology. 27, 1 p.

Research output: Contribution to journalMeeting AbstractResearchpeer-review

Immune Cell Profiling in CML Bone Marrow By Multiplex Immunohistochemistry

Oscar, B., Blom, S., Turkki, R., Kovanen, P. E., Ribeiro, A., Linder, N., Lundin, J., Kallioniemi, O., Pellinen, T. & Mustjoki, S., 2 Dec 2016, In : Blood. 128, 22, 4 p.

Research output: Contribution to journalMeeting AbstractResearchpeer-review

Phase I study with ONCOS-102 for the treatment of solid tumors - an evaluation of clinical response and exploratory analyses of immune markers

Ranki, T., Pesonen, S., Hemminki, A., Partanen, K., Kairemo, K., Alanko, T., Lundin, J., Linder, N., Turkki, R., Ristimäki, A., Jaeger, E., Karbach, J., Wahle, C., Kankainen, M., Backman, C., von Euler, M., Haavisto, E., Hakonen, T., Heiskanen, R., Jaderberg, M. & 6 othersJuhila, J., Priha, P., Suoranta, L., Vassilev, L., Vuolanto, A. & Joensuu, T., 15 Mar 2016, In : Journal for Immunotherapy of Cancer. 4, 18 p., 17.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2015

Assessment of tumour viability in human lung cancer xenografts with texture-based image analysis

Turkki, R., Linder, N., Holopainen, T., Wang, Y., Grote, A., Lundin, M., Alitalo, K. & Lundin, J., Aug 2015, In : Journal of Clinical Pathology. 68, 8, p. 614-621 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Capturing complex tumour biology in vitro: histological and molecular characterisation of precision cut slices

Davies, E., Dong, M., Gutekunst, M., Narhi, K., van Zoggel, H. J. A. A., Blom, S., Nagaraj, A., Metsalu, T., Oswald, E., Erkens-Schulze, S., San Martin, J. A. D., Turkki, R., Wedge, S. R., af Hallstrom, T. M., Schueler, J., van Weerden, W. M., Verschuren, E. W., Barry, S. T., van der Kuip, H. & Hickman, J. A., 9 Dec 2015, In : Scientific Reports. 5, 17 p., 17187.

Research output: Contribution to journalArticleScientificpeer-review

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Immunological data from cancer patients treated with Ad5/3-E2F-Delta 24-GMCSF suggests utility for tumor immunotherapy

Hemminki, O., Parviainen, S., Juhila, J., Turkki, R., Linder, N., Lundin, J., Kankainen, M., Ristimaki, A., Koski, A., Liikanen, I., Oksanen, M., Nettelbeck, D. M., Kairemo, K., Partanen, K., Joensuu, T., Kanerva, A. & Hemminki, A., 28 Feb 2015, In : Oncotarget. 6, 6, p. 4467-4481 15 p.

Research output: Contribution to journalArticleScientificpeer-review

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Open Access
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Repeated intratumoral administration of ONCOS-102 leads to systemic antitumor CD8(+) T-cell response and robust cellular and transcriptional immune activation at tumor site in a patient with ovarian cancer

Vassilev, L., Ranki, T., Joensuu, T., Jaeger, E., Karbach, J., Wahle, C., Partanen, K., Kairemo, K., Alanko, T., Turkki, R., Linder, N., Lundin, J., Ristimaki, A., Kankainen, M., Hemminki, A., Backman, C., Dienel, K., von Euler, M., Haavisto, E., Hakonen, T. & 5 othersJuhila, J., Jaderberg, M., Priha, P., Vuolanto, A. & Pesonen, S., 2015, In : OncoImmunology. 4, 7, 5 p., 1017702.

Research output: Contribution to journalArticleScientificpeer-review

T-cell Subsets in Peripheral Blood and Tumors of Patients Treated With Oncolytic Adenoviruses

Taipale, K., Liikanen, I., Juuso, J., Aila, K-K., Oksanen, M., Turkki, R., Linder, N., Lundin, J., Ristimäki, A., Kanerva, A., Koski, A., Joensuu, T., Vähä-Koskela, M. & Hemminki, A., May 2015, In : Molecular therapy. 23, 5, p. 964-973 10 p.

Research output: Contribution to journalArticleScientificpeer-review

2014

A Malaria Diagnostic Tool Based on Computer Vision Screening and Visualization of Plasmodium falciparum Candidate Areas in Digitized Blood Smears

Linder, N., Turkki, R., Walliander, M., Martensson, A., Diwan, V., Rahtu, E., Pietikainen, M., Lundin, M. & Lundin, J., 21 Aug 2014, In : PLoS One. 9, 8, 12 p., 104855.

Research output: Contribution to journalArticleScientificpeer-review

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Local treatment of a pleural mesothelioma tumor with ONCOS-102 induces a systemic antitumor CD8(+) T-cell response, prominent infiltration of CD8(+) lymphocytes and Th1 type polarization

Ranki, T., Joensuu, T., Jaeger, E., Karbach, J., Wahle, C., Kairemo, K., Alanko, T., Partanen, K., Turkki, R., Linder, N., Lundin, J., Ristimaki, A., Kankainen, M., Hemminki, A., Backman, C., Dienel, K., von Euler, M., Haavisto, E., Hakonen, T., Juhila, J. & 5 othersJaderberg, M., Priha, P., Vassilev, L., Vuolanto, A. & Pesonen, S., 2014, In : OncoImmunology. 3, 10, 4 p., 958937.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2013

An open-source, MATLAB based annotation tool for virtual slides

Turkki, R., Walliander, M., Ojansivu, V., Linder, N., Lundin, M. & Lundin, J., 2013, In : Diagnostic Pathology. 8, Suppl. 1, 4 p., S30.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2012

Identification of tumor epithelium and stroma in tissue microarrays using texture analysis

Linder, N., Konsti, J., Turkki, R., Rahtu, E., Lundin, M., Nordling, F. S. A., Haglund, C., Ahonen, T., Pietikainen, M. & Lundin, J., 2012, In : Diagnostic Pathology. 7, p. Article Number 22 11 p.

Research output: Contribution to journalArticleScientificpeer-review