BioImageXD: an open, general-purpose and high-throughput image-processing platform

    Pasi Kankaanpää, Lassi Paavolainen, Silja Tiitta, Mikko Karjalainen, Joacim Päivärinne, Jonna Nieminen, Varpu Marjomäki, Jyrki Heino, Daniel J White

    Nature Methods (2012)

    Published on December 4, 2025

    DOI: https://doi.org/10.1038/nmeth.2047

    Core: Advanced Imaging Core
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    Genes associated with immune response are upregulated in clinically healthy skin of patients with gliptin-associated bullous pemphigoid
    N. Kokkonen et al. • 2026 • Journal of Investigative Dermatology
    Core:Finnish Functional Genomics Centre
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    Improving genotyped functional screening: A versatile closed-tube PCR for Illumina library generation reduces background sequences in multiplexed sequencing
    S. Oksanen et al. • 2026 • SLAS Technology
    Core:Finnish Functional Genomics Centre
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    Dynamic landscape of transcription initiation by yeast RNA polymerase I
    O. Parilova et al. • 2026 • Nucleic Acids Research
    Abstract RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA, a key step in ribosome biogenesis. Elevated Pol I activity...
    Core:Protein Structure and Chemistry
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    Staphylococcus aureus Augments Epithelial Skin Barrier Damage Through T Cell Activation in Cutaneous T Cell Lymphoma
    M. Gluud et al. • 2026 • Allergy
    ABSTRACT Background Skin barrier dysfunction is central to inflammation and susceptibility to infection in atopic dermatitis (AD). Cutaneous T‐cell lymphoma...
    Core:Cytometry Core
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    Fast label-free live imaging with FlowVision reveals key principles of cancer cell arrest on endothelial monolayers
    G. Follain et al. • 2026 • The EMBO Journal
    Abstract The rapid, transient, and unpredictable nature of interactions between circulating cells and the endothelium challenges the investigation of these...
    Core:Advanced Imaging Core
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    December 4, 2025
    Cytoplasmic keratins couple with and maintain nuclear envelope integrity in colonic epithelial cells
    Carl-Gustaf A. Stenvall, Joel H. Nyström, Ciarán Butler-Hallissey, Theresia Jansson, Taina R. H. Heikkilä, Stephen A. Adam, Roland Foisner, Robert D. Goldman, Karen M. Ridge, Diana M. Toivola Molecular Biology of the Cell (2022)
    Cytoplasmic keratins couple with SUN2 and lamin A at the nuclear envelope and maintain plectin, LINC complex, lamin and lamin-associated...
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    December 4, 2025
    MASTL promotes cell contractility and motility through kinase-independent signaling
    Maria Emilia Taskinen, Elisa Närvä, James R.W. Conway, Laura Soto Hinojosa, Sergio Lilla, Anja Mai, Nicola De Franceschi, Laura L. Elo, Robert Grosse, Sara Zanivan, Jim C. Norman, Johanna Ivaska Journal of Cell Biology (2020)
    Microtubule-associated serine/threonine-protein kinase-like (MASTL) is a mitosis-accelerating kinase with emerging roles in cancer progression. However, possible cell cycle–independent mechanisms behind...
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    December 4, 2025
    [11C]carfentanil PET imaging for studying the peripheral opioid system in vivo: effect of photoperiod on mu-opioid receptor availability in brown adipose tissue
    Lihua Sun, Richard Aarnio, Erika Atencio Herre, Salli Kärnä, Senthil Palani, Helena Virtanen, Heidi Liljenbäck, Jenni Virta, Aake Honkaniemi, Vesa Oikonen, Chunlei Han, Sanna Laurila, Marco Bucci, Semi Helin, Emrah Yatkin, Lauri Nummenmaa, Pirjo Nuutila, Jing Tang, Anne Roivainen European Journal of Nuclear Medicine and Molecular Imaging (2022)
    Abstract Purpose Photoperiod determines the metabolic activity of brown adipose tissue (BAT) and affects the food intake and body mass...
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