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Published results with Anima

  • 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, 2015
    • Detection of vessels and measurement of expression
  • 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
    • Detection of vessels and measurement of morphology
  • Pernilla von Nandelstadh,Erika Gucciardo,Jouko Lohi,Rui Li,Nami Sugiyama,Olli Carpen,and Kaisa Lehti Actin-associated protein palladin promotes tumor cell invasion by linking extracellular matrix degradation to cell cytoskeleton Mol. Biol. Cell mbc.E13-11-0667; First Published on July 2, 2014; doi:10.1091/mbc.E13-11-0667
    • Computer Aided Segmentation of HE-stained tissues, with color clustering approach
  • Ville Rantanen, Miko Valori and Sampsa Hautaniemi, Anima: Modular workflow system for comprehensive image data analysis. Front. Bioeng. Biotechnol. doi: 10.3389/fbioe.2014.00025
    • Use cases of Anima. Main publication of Anima
  • 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, 2014 DOI: 10.1371/journal.pone.0091031
    • Computer Aided Segmentation of HE-stained tissues, with color clustering approach
  • Tatti O., Pekkonen P., Holopainen T., Maliniemi P., Lohi J., Rantanen V., Hautaniemi S., Ranki A., Alitalo K., Ojala P., Keski-Oja J. and Lehti K.: Membrane-type-3 matrix metalloproteinase controls a proteolytic switch between lymphatic and blood vascular invasion of melanoma cells. Manuscript submitted, 2013.
    • Image analysis: Detection of cells and measurement of expression
  • 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
  • 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.
  • 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
  • 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." http://www.ncbi.nlm.nih.gov/pubmed/23684749 Gastroenterology. 2013 Sep 145(3): 540-543.e22. doi: 10.1053/j.gastro.2013.05.015.
    • Image analysis of fluorescent cells
  • 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. http://www.ncbi.nlm.nih.gov/pubmed/23549787
    • Fluorescence image analysis, Colocalization feature extraction and statistics
  • 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. http://www.ncbi.nlm.nih.gov/pubmed/22659387
    • Programming a tool for aided segmentation and feature extraction
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • João Dias et al., Complete list of authors in online publication…, Ville Rantanen, "Targeted Chemotherapy for Head and Neck Cancer with a Chimeric Oncolytic Adenovirus Coding for Bifunctional Suicide Protein FCU1", Clinical Cancer Research. 2010
    • Development of color clustering based approach for brightfield imaging, analysis of images
  • 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.

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