Publications

All publications (Google Scholar): https://scholar.google.com/citations?hl=en&user=MxB3M54AAAAJ&view_op=list_works&sortby=pubdate

PubMed listed publications: https://pubmed.ncbi.nlm.nih.gov/?term=ruusuvuori%2C+p

Publications 2017-2023:

  1. Khan, U., Koivukoski, S., Valkonen, M., Latonen, L, Ruusuvuori, P. The effect of neural network architecture on virtual H&E staining: Systematic assessment of histological feasibility. Patterns, 4, 100725 2023.
  2. Koivukoski, S., Akhtar, U., Ruusuvuori, P., Latonen, L. Unstained tissue imaging and virtual hematoxylin and eosin staining of histological whole slide images. Laboratory Investigation, 103(5), 100070, 2023.
  3. L. Egevad, B. Delahunt, KA. Iczkowski, T. van der Kwast, GJLH. van Leenders, KRM. Leite, C. Pan, H. Samaratunga, T. Tsuzuki, N. Mulliqi, X. Ji, H. Olsson, M. Valkonen, P. Ruusuvuori, M. Eklund, K. Kartasalo. Interobserver Reproducibility of Cribriform Cancer in Prostate Needle Biopsies and Validation of International Society of Urological Pathology Criteria, Histopathology, 82(6):837-845, 2023.
  4. O. Meikar, D. Majoral, O. Heikkinen, E. Valkama, S. Leskinen, A. Rebane, P. Ruusuvuori, J. Toppari, J-A. Mäkelä, N. Kotaja. Stagetool, a novel automated approach for mouse testis histological analysis. Endocrinology, 164 (2), 2023, bqac202
  5. Olsson, H., Kartasalo, K., Capuccini, M., Ruusuvuori, P., Samaratunga, H., Delahunt, B., Lindskog, C., Egevad, L., Spjuth, O., Eklund, M. Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction. Nature Communications, 13, 7761, 2022.
  6. Prezja, F, Pölönen, I., Ruusuvuori, P., Kuopio, T., Väyrynen, J., Äyrämö, S. H&E Multi-Laboratory Staining Variance Exploration with Unsupervised Machine Learning. Applied Sciences,12(15), 7511, 2022
  7. Kartasalo, K., Ström, P., Ruusuvuori, P., Samaratunga, H., Delahunt, B., Tsuzuki, T., Eklund, M., Egevad, L. (2022) Detection of Perineural Invasion in Prostate Needle Biopsies with Deep Neural Networks. Virchows Archiv, 481, pages 73–82 (2022). 
  8. Scaravilli, M., Koivukoski, S., Gillen, A., Bouazza, A., Ruusuvuori, P., Visakorpi, T., Latonen, L. miR-32 promotes MYC-driven prostate cancer. Oncogenesis, 11 (1), 1-10, 2022.
  9. Ruusuvuori, P., Valkonen, M., Kartasalo, K., Visakorpi, T., Nykter, M., Latonen, L. Spatial analysis of histology in 3D: quantification and visualization of organ and tumor level tissue environment, Heliyon, e08762 2022.
  10. Bulten, W., Kartasalo, K., Po-Hsuan C Chen, P Ström, H Pinckaers, K Nagpal, Y Cai, DF. Steiner, H van Boven, R Vink, C Hulsbergen-van de Kaa, J van der Laak, MB. Amin, AJ. Evans, T van der Kwast, R Allan, PA. Humphrey, H Grönberg, H Samaratunga, B Delahunt, T Tsuzuki, T Häkkinen, L Egevad, M Demkin, S Dane, F Tan, M Valkonen, GS. Corrado, L Peng, CH. Mermel, P Ruusuvuori*, G Litjens*, M Eklund*, and the PANDA Challenge consortium. Artificial Intelligence for Diagnosis and Gleason Grading of Prostate Cancer: the PANDA challenge. Nature Medicine, 28, 154–163, 2022.
    *Equal contribution, shared last author
  11. Wang, Y., Kartasalo, K.,, Weitz, P., Acs, B., Valkonen M., Larsson, C., Ruusuvuori, P.*, Hartman, J.*, Rantalainen, M.* (2021). Predicting molecular phenotypes from histopathology images: a transcriptome-wide expression-morphology analysis in breast cancer. Cancer Research, 81(19), 5115-5126.  *Equal contribution, shared last author
  12. Mulliqi, N., Kartasalo, K., Olsson, H., Yi, J., Egevad, L., Eklund, M., Ruusuvuori, P. OpenPhi: An interface to access Philips iSyntax whole slide images for computational pathology. Bioinformatics, 37 (21), 3995-3997, 2021.
  13. Liimatainen, K., Latonen, L., Valkonen, M., Kartasalo, K., Ruusuvuori, P. (2021) Virtual reality for 3D histology: multi-scale visualization of organs with interactive feature exploration. BMC Cancer,  21 (1), 1-14, 2021.
  14. K. Kartasalo, W. Bulten, B. Delahunt, P-HC Chen, H. Pincaers, H. Olsson, X. Ji, N. Mulliqi, H. Samaratunga, T. Tsuzuki, J. Lindberg, M. Rantalainen, C. Wählby, G. Litjens, P. Ruusuvuori, L. Egevad, M. Eklund. Artificial intelligence for Gleason grading of prostate biopsies – current status and next steps. European Urology Focus, 7 (4), 687-691, 2021.
  15. L. Egevad, B. Delahunt, H. Samaratunga, T. Tsuzuki, Y. Yamamoto, J. Yaxley, P. Ruusuvuori, K. Kartasalo, M. Eklund. The Emerging Role of Artificial Intelligence in the Reporting of Prostate Pathology. Pathology, 53 (5), 565-567, 2021.
  16. L. Latonen, P. Ruusuvuori. Building a central repository landmarks a new era for AI-assisted digital pathology development in Europe. European Journal of Cancer, 150, 31-32, 2021.
  17. Liimatainen, K., Huttunen, R., Latonen, L., & Ruusuvuori, P. (2021). Convolutional Neural Network-Based Artificial Intelligence for Classification of Protein Localization Patterns. Biomolecules, 11(2), 264.
  18. Egevad, L., Delahunt, B., Samaratunga, H., Tsuzuki, T., Olsson, H., Ström, P., … & Ruusuvuori, P. (2021). Interobserver reproducibility of perineural invasion of prostatic adenocarcinoma in needle biopsies. Virchows Archiv, 478(6), 1109-1116.
  19. Valkonen, M., Högnäs, G., Bova, G. S., & Ruusuvuori, P. (2021). Generalized fixation invariant nuclei detection through domain adaptation based deep learning. IEEE Journal of Biomedical and Health Informatics, 25(5), 2021.
  20. Mehtonen, J., Teppo, S., Lahnalampi, M., Kokko, A., Kaukonen, R., Oksa, L., … Ruusuvuori, P. … & Heinäniemi, M. (2020). Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities. Genome medicine, 12(1), 1-25.
  21. Borovec, J., Kybic, J., Arganda-Carreras, I., Sorokin, D. V., Bueno, G., Khvostikov, A. V., … & Ruusuvuori, P., … Muñoz-Barrutia, A. (2020). ANHIR: Automatic Non-rigid Histological Image Registration Challenge. IEEE Transactions on Medical Imaging, 39(10), 3042-3052.
  22. Doan, P., Musa, A., Murugesan, A., Sipilä, V., Candeias, N. R., Emmert-Streib, F., Ruusuvuori, P., Granberg, K., Yli-Harja, O., Kandhavelu, M. (2020). Glioblastoma Multiforme Stem Cell Cycle Arrest by Alkylaminophenol through the Modulation of EGFR and CSC Signaling Pathways. Cells, 9(3), 681.
  23. 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. 
  24. S. Eerola, N. Santio, S. Rinne, P. Kouvonen, G. Corthals, M. Scaravilli, G. Scala, A. Serra, D. Greco, P. Ruusuvuori, L. Latonen, E. Raunio, T. Visakorpi, P. Koskinen. Phosphorylation of NFATC1 at PIM1 target sites is essential for its ability to promote prostate cancer cell migration and invasion. Cell Communication and Signaling, 17 (1), 1-16, 2019.
  25. M. 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.
  26. K. 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
  27. K Liimatainen, K. Kartasalo, L Latonen, P Ruusuvuori. 3D-printed whole prostate models with tumor hotspots using dual-extruder printer. In Proc. Of the IEEE EMBC 2019, Berlin, Germany. 4 pages.
  28. K. Kartasalo, L. Latonen.M. Vihinen, T. Visakorpi, M. Nykter, P. Ruusuvuori. Comparative analysis of tissue reconstruction algorithms for 3D histology. Bioinformatics, 34 (17), 3013-3021, 2018. 
  29. G. Högnäs, K. Kivinummi, HML. Kallio, R. Hieta, P. Ruusuvuori, A. Koskenalho, J. Kesseli, T. Tammela, J. Riikonen, J. Ilvesaro, S. Kares, PP. Hirvikoski, M. Laurila, T. Mirtti, M. Nykter, PM. Kujala, T. Visakorpi, T. Tolonen, G.S. Bova. Feasibility of prostate PAXgene fixation for molecular research and diagnostic surgical pathology: Comparison of matched fresh frozen, FFPE and PFPE tissues. The American Journal of Surgical Pathology. 42 (1), 103-115, 2018.
  30. B. 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
    P.R. is a member of the CAMELYON16 Consortium.
  31. L. Latonen, M. Scaravilli, A. Gillen, F-P. Zhang, P. Ruusuvuori, P. Kujala, M. Poutanen, T. Visakorpi. In vivo expression of miR-32 induces proliferation in prostate epithelium. The American Journal of Pathology, 187 (11), 2546-2557, 2017.
  32. M. 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
  33. M. 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
    ^joint first authors
  34. M. Valkonen, K. Kartasalo, K. Liimatainen, M. Nykter, L. Latonen, P. Ruusuvuori. Dual structured convolutional neural network with feature augmentation for quantitative characterization of tissue histology. In Proc. of the International Conference on Computer Vision (ICCV), pp. 27-35, 2017 
  35. KJ. Granberg, M. Annala, B. Lehtinen, J. Kesseli, J. Haapasalo, P. Ruusuvuori, O. Yli-Harja, T. Visakorpi, H. Haapasalo, M. Nykter, W. Zhang. Strong FGFR3 staining is a marker for FGFR3 fusions in diffuse gliomas. Neuro-oncology. 19 (9), 1206-1216, 2017
  36. M. Huttunen, P. Turkki, A. Mäki, L. Paavolainen, P. Ruusuvuori, V. Marjomäki. Echovirus 1 internalization negatively regulates EGFR down-regulation leading to enhanced EGFR signaling. Cellular Microbiology, 19 (3), 2017.

Preprints:

  1. Petäinen, L., Väyrynen, JP., Ruusuvuori, P., Pölönen, I., Äyrämö, S., Kuopio, T.. Domain-specific transfer learning in the automated scoring of tumor-stroma ratio from histopathological images of colorectal cancer. arXiv preprint at arXiv:2212.14652. https://doi.org/10.48550/arXiv.2212.14652
  2. Weitz*, P., Valkonen*, M., Solorzano*, L., Carr, C., Kartasalo, K., Boissin, C., Koivukoski, S., Kuusela, A., Rasic, D., Feng, Y., Pouplier, S., Sharma, A., Ledesma Eriksson, K., Latonen, L., Laenkholm, A-V, Hartman, J.§, Ruusuvuori, P.,§, Rantalainen, M.§ ACROBAT – a multi-stain breast cancer histological whole-slide-image data set from routine diagnostics for computational pathology. arXiv preprint arXiv:2211.13621. https://doi.org/10.48550/arXiv.2211.13621
  3. Honkamaa J., Khan U., Koivukoski S., Latonen L., Ruusuvuori P., Marttinen P. Deformation equivariant cross-modality image synthesis with paired non-aligned training data. arXiv preprint arXiv:2208.12491. 2022.
  4. Y Wang, K Kartasalo, M Valkonen, C Larsson, P. Ruusuvuori*, J. Hartman*, M. Rantalainen*. Predicting molecular phenotypes from histopathology images: a transcriptome-wide expression-morphology analysis in breast cancer. arXiv preprint arXiv:2009.08917, 2020. * equal contribution
  5. J Mehtonen, S Teppo, M Lahnalampi, A Kokko, R Kaukonen, L Oksa, M Bouvy-Liivrand, A Malyukova, S Laukkanen, PI. Mäkinen, S Rounioja, P Ruusuvuori, O Sangfelt, R Lund, T Lönnberg, O Lohi, M Heinäniemi. Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1 positive pediatric leukemia identifies drug-targetable transcription factor activities. bioRxiv, 2020. https://doi.org/10.1101/2020.05.27.116293. 
  6. Ström, P., Kartasalo, K., Ruusuvuori, P., Grönberg, H., Samaratunga, H., Delahunt, B., Tsuzuki, T., Egevad, L., Eklund, M. (2020) Detection of Perineural Invasion in Prostate Needle Biopsies with Deep Neural Networks. arXiv preprint arXiv:2004.01589
  7. K Liimatainen, L Latonen, M Valkonen, K Kartasalo, P. Ruusuvuori. (2020) Virtual reality for 3D histology: multi-scale visualization of organs with interactive feature exploration. arXiv preprint arXiv:2003.11148
  8. Ström, P., Kartasalo, K., Olsson, H., Solorzano, L., Delahunt, B., Berney, D. M., … & Iczkowski, K. A. (2019). Pathologist-Level Grading of Prostate Biopsies with Artificial Intelligence. arXiv preprint arXiv:1907.01368.