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Imaging related

  1. PROX1 is a transcriptional regulator of MMP14, Gramolelli, S., Cheng, J., Martinez-Corral, I., Vähä-Koskela, M., Elbasani, E., Kaivanto, E., Rantanen, V., Tuohinto, K., Hautaniemi, S., Bower, M., Haglund, C., Alitalo, K., Mäkinen, T., Petrova, T. V., Lehti, K. & Ojala, P. M. 22 Jun 2018 In : Scientific Reports. 8, 13 p., 9531
  2. Hyper-phosphorylation of Sequestosome-1 Distinguishes Resistance to Cisplatin in Patient Derived High Grade Serous Ovarian Cancer Cells, Nguyen, E. V., Huhtinen, K., Goo, Y. A., Kaipio, K., Andersson, N., Rantanen, V., Hynninen, J., Lahesmaa, R., Carpen, O. & Goodlett, D. R. Jul 2017 In : Molecular & Cellular Proteomics. 16, 7, p. 1377-1392 16 p.
  3. Deltex-1 mutations predict poor survival in diffuse large B-cell lymphoma, Meriranta, L., Pasanen, A., Louhimo, R., Cervera, A., Alkodsi, A., Autio, M., Taskinen, M., Rantanen, V., Karjalainen-Lindsberg, M-L., Holte, H., Delabie, J., Lehtonen, R., Hautaniemi, S. & Leppä, S. May 2017 In : Haematologica. 102, 5, p. E195-E198 4 p.
  4. Somatic MED12 Nonsense Mutation Escapes mRNA Decay and Reveals a Motif Required for Nuclear Entry, Heikkinen, T., Kämpjärvi, K., Keskitalo, S., von Nandelstadh, P., Liu, X., Rantanen, V., Pitkänen, E., Kinnunen, M., Kuusanmäki, H., Kontro, M., Turunen, M., Mäkinen, N., Taipale, J., Heckman, C., Lehti, K., Mustjoki, S., Varjosalo, M. & Vahteristo, P. Mar 2017 In : Human Mutation. 38, 3, p. 269-274 6 p.
  5. Tatti O, Gucciardo E, Pekkonen P, Holopainen T, Louhimo R, Repo P, Maliniemi P, Lohi J, Rantanen V, Hautaniemi S, Alitalo K, Ranki A, Ojala PM, Keski-Oja J, Lehti K.: MMP16 mediates a proteolytic switch to promote cell-cell adhesion, collagen alignment, and lymphatic invasion in melanoma. Cancer Res. 2015 Mar 25. pii: canres.1923.2014.
    • Image analysis: Detection of cells and measurement of expression
  6. Doctoral Thesis: Integration platform for biomedical image analysisRantanen, V. 2015 [V. Rantanen]. 41 p.
  7. Norrmén C, Figlia G, Lebrun-Julien F, Pereira JA, Trötzmüller M, Köfeler HC, Rantanen V, Wessig C, van Deijk AL, Smit AB, Verheijen MH, Rüegg MA, Hall MN, Suter U., "mTORC1 Controls PNS Myelination along the mTORC1-RXRγ-SREBP-Lipid Biosynthesis Axis in Schwann Cells.", Cell Reports, 2014 Oct 7, DOI:10.1016/j.celrep.2014.09.001
    • Image analysis: Detection of vessels and measurement of morphology
  8. Olli S. Mattila*, Ville Rantanen*, Jani Saksi, Daniel Strbian, Tero Pikkarainen, Sampsa Hautaniemi, Perttu J. Lindsberg, "Workflow for automated quantification of cerebromicrovascular gelatinase activity", Microvascular Research, Accepted Aug.2014
    • Image analysis: Detection of vessels and measurement of expression
  9. Ville Rantanen, Miko Valori, Sampsa Hautaniemi. "Anima: Modular workflow system for comprehensive image data analysis" Front. Bioeng. Biotechnol. doi: 10.3389/fbioe.2014.00025. Accepted for publication July 2014
    • Publication of the ANIMA toolbox, with which all of the previous analysis have been developed.
  10. Minna Taskinen, Riku Louhimo, Satu Koivula, Ping Chen, Ville Rantanen, Harald Holte, Jan Delabie, Marja-Liisa Karjalainen-Lindsberg,Magnus Björkholm, Øystein Fluge, Lars Møller Pedersen, Karin Fjordén, Mats Jerkeman, Mikael Eriksson, Sampsa Hautaniemi, Sirpa Leppä. "Deregulation of COMMD1 Is Associated with Poor Prognosis in Diffuse Large B-cell Lymphoma" PLOS One, March 13, 2014DOI: 10.1371/journal.pone.0091031
    • Computer Aided Segmentation of HE-stained tissues, with color clustering approach
  11. Af Hällström TM, Zhao H, Tian J, Rantanen V, Reese SW, Nolley R, Laiho M, Peehl DM. "A Tissue Graft Model of DNA Damage Response in the Normal and Malignant Human Prostate.", J Urol. 2013 Sep 10. doi:10.1016/j.juro.2013.09.007.
    • A pipeline capable of splitting up >gigapixel whole tissue images, with a computer aided color clustering algorithm for multiclass threshold
  12. Niko Aarne, Janne Laine, Tuomas Hänninen, Ville Rantanen, Jani Seitsonen, Janne ruokolainen and Eero Kontturi "Controlled hydrophobic functionalization of natural fibers by self-assembly of amphiphilic diblock copolymer micelles", ChemSusChem 2013, doi:10.1002/cssc.201300218
    • Image analysis. Applying a Gaussian blob detector to find circular texture objects from a noisy image source.
  13. Olli Matilainen, Leena Arpalahti, Ville Rantanen, Sampsa Hautaniemi, Carina I. Holmberg, "Insulin/IGF-1 Signaling Regulates Proteasome Activity through the Deubiquitinating Enzyme UBH-4", Cell Reports 3(6) pp. 1980 - 1995, 2013
    • Granular intracellular object detector
  14. Gylfe AE, Kondelin J, Turunen M, Ristolainen H, Katainen R, Pitkänen E, Kaasinen E, Rantanen V, Tanskanen T, Varjosalo M, Lehtonen H, Palin K, Taipale M, Taipale J, Renkonen-Sinisalo L, Järvinen H, Böhm J, Mecklin JP, Ristimäki A, Kilpivaara O, Tuupanen S, Karhu A, Vahteristo P, Aaltonen LA."Identification of candidate oncogenes in human colorectal cancers with microsatellite instability." Gastroenterology. 2013 Sep;145(3):540-543.e22. doi:10.1053/j.gastro.2013.05.015. Epub 2013 May 16.
    • Image analysis of fluorescent cells
  15. Ylivinkka I, Hu Y, Chen P, Rantanen V, Hautaniemi S, Nyman TA, Keski-Oja J, Hyytiäinen M., "Netrin-1 induced activation of Notch signaling mediates glioblastoma cell invasion." J Cell Sci. 2013 Apr 2. doi: 10.1242/jcs.120022.
    • Fluorescence image analysis, Colocalization feature extraction and statistics
  16. Jalkanen SE (Hernesniemi), Lahesmaa-Korpinen AM, Heckman CA, Rantanen V, Porkka K, Hautaniemi S, Mustjoki S. Phosphoprotein profiling predicts response to tyrosine kinase inhibitor therapy in chronic myeloid leukemia patients. Exp Hematol. 2012 Jun 1. doi: 10.1016/j.exphem.2012.05.010
    • Programming a tool for aided segmentation and feature extraction
  17. Fang Cheng, Pirita Pekkonen, Simonas Laurinavicius, Nami Sugiyama, Stephen Henderson, Thomas Günther, Ville Rantanen, Elisa Kaivanto, Mervi Aavikko, Grzegorz Sarek, Sampsa Hautaniemi, Peter Biberfeld, Lauri Aaltonen, Adam Grundhoff, Chris Boshoff, Kari Alitalo, Kaisa Lehti, Päivi M. Ojala "KSHV-Initiated Notch Activation Leads to Membrane-Type-1 Matrix Metalloproteinase-Dependent Lymphatic Endothelial-to-Mesenchymal Transition", Cell Host & Microbe, Volume 10, Issue 6, 577-590, 15 December 2011
    • Analysis of dendrite images, feature extraction
  18. Sari Jäämaa, Anna Sankila, Ville Rantanen, Karita Peltonen, Päivi M Järvinen, Taija M Af Hällström, Mirja Ruutu, Kimmo Taari, Leif C Andersson, Marikki Laiho "Contrasting DNA damage checkpoint responses in epithelium of the human seminal vesicle and prostate", The Prostate, 11/2011; DOI: 10.1002/pros.21509
    • Analysis of fluorescent tissue images, feature extraction, conclusions with clustering and decision algorithms
  19. Hans Blom, Daniel Rönnlund, Lena Scott, Zuzana Spicarova, Ville Rantanen, Jerker Widengren, Anita Aperia, Hjalmar Brismar "Nearest neighbor analysis of dopamine D1 receptors and Na+-K+-ATPases in dendritic spines dissected by STED microscopy", Microscopy Research and Technique, 2011 ( doi:10.1002/jemt.21046
    • Development of self-self/self-other neighbor algorithm, and performing the analysis
  20. Henna M. Moore, Bayoan Bai, François-Michel Boisvert, Leena Latonen, Ville Rantanen, Jeremy C. Simpson, Rainer Pepperkok, Angus I. Lamond and Marikki Laiho "Quantitative proteomics and dynamic imaging of the nucleolus reveals distinct responses to UV and ionizing radiation", MCP Molecular & Cellular Proteomics, July 21, 2011.
    • Development of livecell timeseries analysis, performing the analysis
  21. Olli S. Mattila, MB*; Daniel Strbian, MD, PhD*; Jani Saksi, BSc*; Tero O. Pikkarainen, BSc; Ville Rantanen, MSc; Turgut Tatlisumak, MD, PhD; Perttu J. Lindsberg, MD, PhD "Cerebral mast cells mediate blood-brain barrier disruption in acute experimental ischemic stroke through perivascular gelatinase activation", STROKE, 2011
    • Performing the analysis on fluorescent tissue images
  22. Sari Jäämaa, Taija Kiviharju-af Hällström, Anna Sankila, Ville Rantanen, Hannu Koistinen, Ulf-Hakan Stenman, Zhewei Zhang, Zhiming Yang, Angelo De Marzo, Kimmo Taari, Mirja Ruutu, Leif Andersson, and Marikki Laiho, "DNA Damage Recognition via Activated ATM and p53 Pathway in Non-proliferating Human Prostate Tissue" ,Cancer Research, 2010
    • Development of the method, Analysis of fluorescent tissue images, feature extraction, conclusions with clustering and decision algorithms
  23. Emma M. Savilahti, MD, Ville Rantanen ,MSc, Jing Lin , PhD, Sirkku Karinen, MSc, Kristiina M. Saarinen, MD PhD, Marina Goldis, MD, Mika Mäkelä, MD PhD, Sampsa Hautaniemi, DTech, Erkki Savilahti, MD PhD, Hugh Sampson, MD “Early recovery from cow's milk allergy is associated with decreasing IgE and increasing IgG4 binding to cow's milk epitopes” the Journal of Allergy and Clinical Immunology. 2010
    • Analysis of fluorescent protein array images, feature/quality extraction, analysis of data
  24. Dias JD1, Liikanen I, Guse K, Foloppe J, Sloniecka M, Diaconu I, Rantanen V, Eriksson M, Hakkarainen T, Lusky M, Erbs P, Escutenaire S, Kanerva A, Pesonen S, Cerullo V, Hemminki A., "Targeted chemotherapy for head and neck cancer with a chimeric oncolytic adenovirus coding for bifunctional suicide protein FCU1." Clin Cancer Res. 2010 May 1;16(9):2540-9. doi: 10.1158/1078-0432.CCR-09-2974.
    • Development of color clustering based approach for brightfield imaging, analysis of images
  25. MSc. Anna Enzerink, Ville Rantanen, Antti Vaheri, "Fibroblast nemosis induces angiogenic responses of endothelial cells." ECR-09-493R1, Experimental Cell Research. 2009 / 11
    • Development of clustering based approach for wounding experiments. Developing a GUI around the method.

Other

  1. Vilma Aho, Hanna M. Ollila, Ville Rantanen, Erkki Kronholm, Ida Surakka, Wessel M. A. van Leeuwen, Maili Lehto, Sampsa Matikainen, Samuli Ripatti, Mikko Härmä, Mikael Sallinen, Veikko Salomaa, Matti Jauhiainen, Harri Alenius, Tiina Paunio, Tarja Porkka-Heiskanen. "Partial Sleep Restriction Activates Immune Response-Related Gene Expression Pathways: Experimental and Epidemiological Studies in Humans", PLOS ONE 2013 DOI: 10.1371/journal.pone.0077184
    • Gene pathway/ontology analysis
  2. Anna-Maria Lahesmaa-Korpinen, Sari E. Jalkanen, Ping Chen, Erkka Valo, Javier Núñez-Fontarnau, Ville Rantanen, Ali Oghabian, Jukka Vakkila, Kimmo Porkka, Satu Mustjoki and Sampsa Hautaniemi "FlowAnd: Comprehensive Computational Framework for Flow Cytometry Data Analysis", J Proteomics Bioinform 2011, 4:197 doi: 10.4172/jpb.1000197
    • Programming of the backbone tools
  3. Elli Leppä, Anni-Maija Linden, Olga Y. Vekovischeva, Ville Rantanen, Esko Toppila, Harald Höger, Werner Sieghart, Peer Wulff, William Wisden, Esa R. Korpi* "Removal of GABAA Receptor gamma2 Subunits from Parvalbumin Neurons Causes Wide-ranging Behavioral Alterations", PLoS One, 2011
    • Development of a GUI program for analysing tremor data
  4. Kristian Ovaska, Marko Laakso, Saija Haapa-Paananen, Riku Louhimo, Ping Chen, Viljami Aittomäki,Erkka Valo, Javier Núñez-Fontarnau1, Ville Rantanen, Sirkku Karinen, Kari Nousiainen, Anna-Maria Lahesmaa-Korpinen, Minna Miettinen, Lilli Saarinen, Pekka Kohonen, Jianmin Wu1, Jukka Westermarck and Sampsa Hautaniemi* "Large-scale data integration framework provides a comprehensive view on glioblastoma", Genome Medicine 2010
    • Development of several modules, documentation, testing suites and general tools
  5. Rajecki M, af Hällström T, Hakkarainen T, Nokisalmi P, Hautaniemi S, Nieminen AI, Tenhunen M, Rantanen V, Desmond RA, Chen DT, Guse K, Stenman UH, Gargini R, Kapanen M, Klefström J, Kanerva A, Pesonen S, Ahtiainen L, Hemminki A. "Mre11 inhibition by oncolytic adenovirus associates with autophagy and underlies synergy with ionizing radiation", International Journal of Cancer, 2009 Nov 15;125(10):2441-9. doi: 10.1002/ijc.24608.
    • Microarray analysis

 

Patent

  1. Metadata associated with a printed image, Inventors:  Hannu Saarelma, Pirkko Oittinen, Ville Rantanen, Publication date: 2010-07-22, Patent application number: 20100185598

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