Max Planck Institute for Multidisciplinary Sciences

Publications

Journal Article (119)

1.

Journal Article

Scodellaro, R.; Zschüntzsch, J.; Hell, A.-K.; Alves, F.: A first explainable-AI-based workflow integrating forward-forward and backpropagation-trained networks of label-free multiphoton microscopy images to assess human biopsies of rare neuromuscular disease. Computer Methods and Programs in Biomedicine 265, 108733 (2025)

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Papantonis, A.; Rogalla, S.; Dullin, C.; Alves, F.; Bohnenberger, H.: Neue Methoden am Übergang von der Forschung in die Routinediagnostik. Die Pathologie 46, pp. 156 - 162 (2025)

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Ferrari, D. P.; Cobanoglu, O.; Sayedipour, S.; Luna, O.; Ferkel, S. A. M.; Agorku, D.; Perez, Y.; Cruz, L. J.; Albericio, F.; Trottein, F. et al.; Alves, F.; Markus, M. A.; Ramos Gomes, F.: Anti-Tumor Efficacy of a Mesothelin-Based Nanovaccine in a KPC Orthotopic Mouse Model of Pancreatic Cancer. Vaccines 13 (3), 314 (2025)

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Sagar, M. M. R.; D'Amico, L.; Longo, E.; Persson, I. M.; Deyhle, R.; Tromba, G.; Bayat, S.; Alves, F.; Dullin, C.: Air artifact suppression in phase contrast micro-CT using conditional generative adversarial networks. Journal of Synchrotron Radiation (accepted)

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Dullin, C.; Alves, F.: Einsatz von künstlicher Intelligenz in der Endoskopie zur Analyse von Gewebebiopsien. Die Gastroenterologie 20, pp. 44 - 53 (2025)

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Ferreira, N.; Kulkarni, A.; Agorku, D.; Midelashvili, T.; Hardt, O.; Legler, T. J.; Ströbel, P.; Conradi, L.-C.; Alves, F.; Ramos Gomes, F. et al.; Markus, M. A.: OrganoIDNet: a deep learning tool for identification of therapeutic effects in PDAC organoid-PBMC co-cultures from time-resolved imaging data. Cellular Oncology 48, pp. 101 - 122 (2025)

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Frohn, J.; Böddeker, F.; Reichardt, M.; Bruns, H.; Czajka, T.; Khan, A.; Broche, L.; Krisch, M.; Bravin, A.; Alves, F. et al.; Zschüntzsch, J.; Salditt, T.: Three-dimensional structure of entire hydrated murine hearts at histological resolution. Scientific Reports 15, 2766 (2025)

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8.

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Nolte, P.; Gröger, C. J.; Frey, C.; Richter, H.; Will, F.; Bäuerle, T.; Schilling, A. F.; Alves, F.; Rußmann, C.; Dullin, C.: Automated Targeted Sectioning of Resin-embedded Hard Tissue Specimen Using Micro-computed Tomography in Combination with Laser Microtomy. IEEE Transactions on Biomedical Engineering (2025)

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Napp, J.; Siebel, P.; Rausch, H.; Kuchta, K.; Efferth, T.; Alves, F.; Ellenrieder, V.; Cameron, S.: Prolonged survival by combination treatment with a standardized herbal extract from Japanese Kampo-medicine (Juzentaihoto) and gemcitabine in an orthotopic transplantation pancreatic cancer model. Frontiers in Oncology 14, 1454291 (2024)

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Notter, S.; Choezom, D.; Griebel, T.; Ramos Gomes, F.; Möbius, W.; De Oliveira, T.; Conradi, L.-C.; Alves, F.; Feldmann, C.: High-Load Core@Shell Nanocarriers with Irinotecan and 5-Fluorouracil for Combination Chemotherapy in Colorectal Cancer. Small Science 4 (11), 2400196 (2024)

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11.

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Arora, B.; Kulkarni, A.; Markus, M. A.; Ramos Gomes, F.; Bohnenberger, H.; Ströbel, P.; Alves, F.; Klein, O.: MALDI imaging combined with two-photon microscopy reveals local differences in the heterogeneity of colorectal cancer. npj Imaging 2, 35 (2024)

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Tan, L.; Zschüntzsch, J.; Meyer, S.; Stobbe, A.; Bruex, H.; Regensburger, A. P.; Claßen, M.; Alves, F.; Jüngert, J.; Rother, U. et al.; Li, Y.; Danko, V.; Lang, W.; Türk, M.; Schmidt, S.; Vorgerd, M.; Schlaffke, L.; Woelfle, J.; Hahn, A.; Mensch, A.; Winterholler, M.; Trollmann, R.; Heiß, R.; Wagner, A. L.; Raming, R.; Knieling, F.: Non-invasive optoacoustic imaging of glycogen-storage and muscle degeneration in late-onset Pompe disease. Nature Communications 15, 7843 (2024)

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13.

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Agorku, D. J.; Bosio, A.; Alves, F.; Ströbel, P.; Hardt, O.: Colorectal cancer-associated fibroblasts inhibit effector T cells via NECTIN2 signaling. Cancer Letters 595, 216985 (2024)

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Kulkarni, A.; Ferreira, N.; Scodellaro, R.; Choezom, D.; Alves, F.: A Curated Cell Life Imaging Dataset of Immune-enriched Pancreatic Cancer Organoids with Pre-trained AI Models. Scientific Data 11, 820 (2024)

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15.

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Sabljo, K.; Ischyropoulou, M.; Napp, J.; Alves, F.; Feldmann, C.: High-load nanoparticles with a chemotherapeutic SN-38/FdUMP drug cocktail. Nanoscale 16, pp. 14853 - 14860 (2024)

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16.

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Ferrari, D. P.; Ramos Gomes, F.; Alves, F.; Markus, M. A.: KPC-luciferase-expressing cells elicit an anti-tumor immune response in a mouse model of pancreatic cancer. Scientific Reports 14, 13602 (2024)

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17.

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Arora, B.; Kulkarni, A.; Markus, M. A.; Ströbel, P.; Bohnenberger, H.; Alves, F.; Ramos-Gomes, F.: Label-free quantification of imaging features in the extracellular matrix of left and right-sided colon cancer tissues. Scientific Reports 14, 7510 (2024)

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18.

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Dullin, C.; Albers , J.; Tagat, A.; Lorenzon, A.; D'Amico, L.; Chiriotti, S.; Sodini, N.; Dreossi, D.; Alves, F.; Bergamaschi, A. et al.; Tromba, G.: In vivo low-dose phase-contrast CT for quantification of functional and anatomical alterations in lungs of an experimental allergic airway disease mouse model. Frontiers in medicine 11, 1338846 (2024)

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19.

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D'Amico, L.; Svetlove, A.; Longo, E.; Meyer, R.; Senigagliesi, B.; Saccomano, G.; Nolte, P.; Wagner, W. L.; Wielpuetz, M. O.; Leitz, D. H. W. et al.; Duerr, J.; Mall, M. A.; Casalis, L.; Köster, S.; Alves, F.; Tromba, G.; Dullin, C.: Characterization of transient and progressive pulmonary fibrosis by spatially correlated phase contrast microCT, classical histopathology and atomic force microscopy. Computers in Biology and Medicine 169, 107947 (2024)

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20.

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Luna, O. F.; Perez, Y. V.; Ferrari, D. P.; Sayedipour, S. S.; Royo, M.; Acosta, G. A.; Cruz, L. J.; Alves, F.; Agner, E.; Sydnes, M. O. et al.; Albericio, F.: Impact of N-Terminal PEGylation on Synthesis and Purification of Peptide-Based Cancer Epitopes for Pancreatic Ductal Adenocarcinoma (PDAC). ACS Omega 9 (32), pp. 34544 - 34554 (2024)

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21.

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Rudolph, D.; Ischyropoulou, M.; Pfeifer, J.; Napp, J.; Schepers, U.; Alves, F.; Feldmann, C.: Cocktail of lipophilic and hydrophilic chemotherapeutics in high-load core@shell nanocarriers to treat pancreatic tumours. Nanoscale Advances 6, pp. 973 - 984 (2024)

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22.

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Sagar, M. M. R.; Svetlove, A.; D’Amico, L.; Pinkert-Leetsch, D.; Missbach-Guentner, J.; Longo, E.; Tromba, G.; Bohnenberger, H.; Alves, F.; Dullin, C.: Optical clearing: an alternative sample preparation method for propagation based phase contrast μCT. Frontiers in Physics 12, 1433895 (2024)

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23.

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Cobanoglu, O.; Delval, L.; Ferrari, D. P.; Deruyter, L.; Heumel, S.; Wolowczuk, I.; Hussein, A.; Menevse, A. N.; Bernard, D.; Beckhove, P. et al.; Alves, F.; Trottein, F.: Depletion of preexisting B-cell lymphoma 2-expressing senescent cells before vaccination impacts antigen-specific antitumor immune responses in old mice. Aging Cell 22 (12), e14007 (2023)

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24.

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Garnier, N.; Berghout, J.; Zygmunt, A.; Singh, D.; Huang, K. A.; Kantz, W.; Blankart, C. R.; Gillner, S.; Zhao, J.; Roettger, R. et al.; Saier, C.; Kirschner, J.; Schenk, J.; Atkins, L.; Ryan, N.; Zarakowska, K.; Zschuentzsch, J.; Zuccolo, M.; Muellenborn, M.; Man, Y.-S.; Goodman, L.; Trad, M.; Chalandon, A. S.; Sansen, S.; Martinez-Fresno, M.; Badger, S.; Walther van Olden, R.; Rothmann, R.; Lehner, P.; Tschohl, C.; Baillon, L.; Gumus, G.; Gross, E.; Stefanov, R.; Iskrov, G.; Raycheva, R.; Kostadinov, K.; Mitova, E.; Einhorn, M.; Einhorn, Y.; Schepers, J.; Huebner, M.; Alves, F.; Iskandar, R.; Mayer, R.; Renieri, A.; Piperkova, A.; Gut, I.; Beltran, S.; Matthiesen, M. E.; Poetz, M.; Hansson, M.; Trollmann, R.; Agolini, E.; Ottombrino, S.; Novelli, A.; Bertini, E.; Selvatici, R.; Farne, M.; Fortunato, F.; Ferlini, A.: Genetic newborn screening and digital technologies: A project protocol based on a dual approach to shorten the rare diseases diagnostic path in Europe. PLOS ONE 18 (11), e0293503 (2023)

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25.

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Ischyropoulou, M.; Sabljo, K.; Schneider, L.; Niemeyer, C. M.; Napp, J.; Feldmann, C.; Alves, F.: High‐Load Gemcitabine Inorganic–Organic Hybrid Nanoparticles as an Image‐Guided Tumor‐Selective Drug‐Delivery System to Treat Pancreatic Cancer. Advanced Materials 35 (46), 2305151 (2023)

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26.

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Khan, A.; Markus, M. A.; Svetlove, A.; Hülsmann, S.; Alves, F.; Dullin, C.: Longitudinal x-ray based lung function measurement for monitoring Nintedanib treatment response in a mouse model of lung fibrosis. Scientific Reports 13 (1), 18637 (2023)

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27.

Journal Article

Nolte, P.; Brettmacher, M.; Gröger, C. J.; Gellhaus, T.; Svetlove, A.; Schilling, A. F.; Alves, F.; Russmann, C.; Dullin, C.: Spatial correlation of 2D hard-tissue histology with 3D microCT scans through 3D printed phantoms. Scientific Reports 13 (1), 18479 (2023)

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28.

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Markus, M. A.; Ferrari, D. P.; Alves, F.; Ramos Gomes, F.: Effect of tissue fixation on the optical properties of structural components assessed by non-linear microscopy imaging. Biomedical Optics Express 14 (8), pp. 3988 - 4002 (2023)

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29.

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Pinkert-Leetsch, D.; Frohn, J.; Ströbel, P.; Alves, F.; Salditt, T.; Missbach-Guentner, J.: Three-dimensional analysis of human pancreatic cancer specimens by phase-contrast based X-ray tomography – the next dimension of diagnosis. Cancer Imaging 23, 43 (2023)

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30.

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Pantelaiou-Prokaki, G.; Reinhardt, O.; Georges, N. S.; Agorku, D. J.; Hardt, O.; Prokakis, E.; Mieczkowska, I. K.; Deppert, W.; Wegwitz, F.; Alves, F.: Basal-like mammary carcinomas stimulate cancer stem cell properties through AXL-signaling to induce chemotherapy resistance. International Journal of Cancer 152 (9), pp. 1916 - 1932 (2023)

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31.

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Czaplinska, D.; Ialchina, R.; Andersen, H. B.; Yao, J.; Stigliani, A.; Dannesboe, J.; Flinck, M.; Chen, X.; Mitrega, J.; Gnosa, S. P. et al.; Dmytriyeva, O.; Alves, F.; Napp, J.; Sandelin, A.; Pedersen, S. F.: Crosstalk between tumor acidosis, p53 and extracellular matrix regulates pancreatic cancer aggressiveness. International Journal of Cancer 152 (6), pp. 1210 - 1225 (2023)

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32.

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Albers, J.; Wagner, W. L.; Fiedler, M. O.; Rothermel, A.; Wuennemann, F.; Di Lillo, F.; Dreossi, D.; Sodini, N.; Baratella, E.; Confalonieri, M. et al.; Arfelli, F.; Kalenka, A.; Lotz, J.; Biederer, J.; Wielpuetz, M. O.; Kauczor, H.-U.; Alves, F.; Tromba, G.; Dullin, C.: High resolution propagation-based lung imaging at clinically relevant X-ray dose levels. Scientific Reports 13 (1), 4788 (2023)

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33.

Journal Article

Khorenko, M.; Pfeifer, J.; Napp, J.; Meschkov, A.; Alves, F.; Schepers, U.; Feldmann, C.: Theranostic inorganic–organic hybrid nanoparticles with a cocktail of chemotherapeutic and cytostatic drugs. Journal of Materials Chemistry B 11, pp. 3635 - 3649 (2023)

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34.

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Nolte, P.; Dullin, C.; Svetlove, A.; Brettmacher, M.; Russmann, C.; Schilling, A. F.; Alves, F.; Stock, B.: Current Approaches for Image Fusion of Histological Data with Computed Tomography and Magnetic Resonance Imaging. Radiology Research and Practice 2022, 6765895 (2022)

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35.

Journal Article

Ritschel, C.; Napp, J.; Alves, F.; Feldmann, C.: Monitoring nanoparticle dissolution via fluorescence-colour shift. Nanoscale 14 (43), pp. 16249 - 16255 (2022)

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36.

Journal Article

Pinkert-Leetsch, D.; Rost, J. U.; Schmiedeknecht, M. U. H.; Stadelmann, C.; Alves, F.; Missbach-Guentner, J.: The murine male reproductive organ at a glance: Three-dimensional insights and virtual histology using label-free light sheet microcopy. Andrology 10 (8), pp. 1660 - 1672 (2022)

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37.

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Werner, M.; Dyas, A.; Parfentev, I.; Schmidt, G. E.; Mieczkowska, I. K.; Müller-Kirschbaum, L. C.; Müller, C.; Kalkhof, S.; Reinhardt, O.; Urlaub, H. et al.; Alves, F.; Gallwas, J.; Prokakis, E.; Wegwitz, F.: ROBO3s: a novel ROBO3 short isoform promoting breast cancer aggressiveness. Cell Death and Disease 13, 762 (2022)

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38.

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Dullin, C.; Svetlove, A.; Zschuntzsch, J.; Alves, F.: Simultaneous assessment of lung morphology and respiratory motion in retrospectively gated in-vivo microCT of free breathing anesthetized mice. Scientific Reports 12 (1), 13299 (2022)

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39.

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Pfeifer, R.; Henze, J.; Wittich, K.; Gosselink, A.; Kinkhabwala, A.; Gremse, F.; Bleilevens, C.; Bigott, K.; Jungblut, M.; Hardt, O. et al.; Alves, F.; Al Rawashdeh, W.: A multimodal imaging workflow for monitoring CAR T cell therapy against solid tumor from whole-body to single-cell level. Theranostics 12 (11), pp. 4834 - 4850 (2022)

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40.

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Hermasch, M. A.; Janning, H.; Perera, R. P.; Schnabel, V.; Rostam, N.; Ramos Gomes, F.; Muschalek, W.; Bennemann, A.; Alves, F.; Ralser, D. J. et al.; Betz, R. C.; Schön, M. P.; Dosch, R.; Frank, J.: Evolutionary distinct roles of γ-secretase subunit nicastrin in zebrafish and humans. Journal of Dermatological Science 105 (2), pp. 80 - 87 (2022)

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41.

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Ramos-Gomes, F.; Ferreira, N.; Alves, F.; Markus, M. A.: An alternative technique for monitoring the live interaction of monocytes and tumor cells with nanoparticles in the mouse lung. Bio-protocol 12 (2), e4293 (2022)

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42.

Journal Article

Sabljo, K.; Napp, J.; Alves, F.; Feldmann, C.: pH-Dependent fluorescence of [La(OH)₂]⁺[ARS]^- hybrid nanoparticles for intracellular pH-sensing. Chemical Communications 58 (67), pp. 9417 - 9420 (2022)

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43.

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Svetlove, A.; Albers, J.; Huelsmann, S.; Markus, M. A.; Zschuentzsch, J.; Alves, F.; Dullin, C.: Non-Invasive Optical Motion Tracking Allows Monitoring of Respiratory Dynamics in Dystrophin-Deficient Mice. Cells 11 (5), 918 (2022)

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44.

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Khan, A.; Ramos Gomes, F.; Markus, M. A.; Mietsch, M.; Hinkel, R.; Alves, F.: Label-free imaging of age-related cardiac structural changes in non-human primates using multiphoton nonlinear microscopy. Biomedical Optics Express (2021)

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45.

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Götze, T.; Soto-Bernardini, M. C.; Zhang, M.; Mießner, H.; Linhoff, L.; Brzózka, M. M.; Velanac, V.; Dullin, C.; Ramos Gomes, F.; Peng, M. et al.; Husseini, H.; Schifferdecker, E.; Fledrich, R.; Sereda, M. W.; Willig, K.; Alves, F.; Rossner, M. J.; Nave, K.-A.; Zhang, W.; Schwab, M. H.: Hyperactivity is a Core Endophenotype of Elevated Neuregulin-1 Signaling in Embryonic Glutamatergic Networks. SCHIZOPHRENIA BULLETIN 47 (5), pp. 1409 - 1420 (2021)

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46.

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Sier, V. Q.; de Vries, M. R.; van der Vorst, J. R.; Vahrmeijer, A. L.; van Kooten, C.; Cruz, L. J.; de Geus-Oei, L.-F.; Ferreira, V.; Sier, C. F. M.; Alves, F. et al.; Muthana, M.: Cell-based tracers as trojan horses for image-guided surgery. International Journal of Molecular Sciences 22 (2), 755 (2021)

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47.

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Albers, J.; Svetlove, A.; Alves, J.; Kraupner, A.; di Lillo, F.; Markus, A.; Tromba, G.; Alves, F.; Dullin, C.: Elastic transformation of histological slices allows precise co-registration with microCT data sets for a refined virtual histology approach. Scientific Reports 11, 10846 (2021)

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48.

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Dullin, C.; di Lillo, F.; Svetlove, A.; Albers, J.; Wagner, W.; Markus, A.; Sodini, N.; Dreossi, D.; Alves, F.; Tromba, G.: Multiscale biomedical imaging at the SYRMEP beamline of Elettra - Closing the gap between preclinical research and patient applications. Physics Open 6, 100050, p. 100050 (2021)

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49.

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Khan, A.; Markus, A.; Rittmann, T.; Albers, J.; Alves, F.; Hülsmann, S.; Dullin, C.: Simple low dose radiography allows precise lung volume assessment in mice. Scientific Reports 11, 4163 (2021)

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50.

Journal Article

Ramos Gomes, F.; Ferreira, N.; Kraupner, A.; Alves, F.; Markus, A.: Ex vivo Live Cell Imaging of Nanoparticle-Cell Interactions in the Mouse Lung. Frontiers in Bioengineering and Biotechnology 8 (2020)

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