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Research

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Table of Contents

For a full list of publications, see Orcid , Google Scholar .

Theses #

  1. Ph. D. Thesis, Ben Cardoen, School of Computing Science, Simon Fraser University, Canada, 2024-04-30, ‘as-is’ accepted. Computational reconstruction of multiscale interaction in multichannel superresolution microscopy

  2. M.Sc. Thesis, Ben Cardoen, Department of Computer Science, University of Antwerp, Belgium 2017-06-30, ‘with highest distinction’ accepted. Convergence of distributed symbolic regression using metaheuristics DOI >

  3. B.Sc. Thesis, Ben Cardoen, Department of Computer Science, University of Antwerp, Belgium 2015-06-30, ‘with high distinction’ accepted. A Parallel Discrete Event Simulator in C++

Note: The bold author highlights are for visual purposes only. PDF copies are author copies, distribution may not be allowed, personal use only.

Journal #

  1. New! Ivan Robert Nabi, Ben Cardoen, Khater, Guang Gao, Timothy H. Wong, and Ghassan Hamarneh. AI-based analysis of super-resolution microscopy: Biological discovery in the absence of ground truth. The Journal Of Cell Biology (JCB), 10.1083/jcb.202311073, 2024

  2. New! Hanene Ben Yedder, Ben Cardoen, Majid Shokoufi, Farid Golnaraghi, and Ghassan Hamarneh. Deep Orthogonal Multi-Wavelength Fusion for Tomogram-Free Diagnosis in Diffuse Optical Imaging. Computers in Biology and Medicine (CIBM), 10.1016/j.compbiomed.2024.108676000:000, 2024

  3. Ben Cardoen, Kurt Vandevoorde, Guang Gao, Milene Ortiz-Silva, Parsa Alan, Ellie Tiliakou, William Liu, A. Wayne Vogl, Ghassan Hamarneh, and Ivan Robert Nabi. Membrane contact site detection (MCS-DETECT) reveals dual control of rough mitochondria-ER contacts (Cardoen, Vandevoorde, Gao, and Ortiz: Joint first authors; Hamarneh and Nabi: Joint senior authors). The Journal Of Cell Biology (JCB), 10.1083/jcb.202206109:000-000, 11 2023.

  4. Ben Cardoen, Hanene Ben Yedder, Sieun Lee, Ivan Robert Nabi, and Ghassan Hamarneh. DataCurator.jl: Efficient, portable, and reproducible validation, curation, and transformation of large heterogeneous datasets using human-readable recipes compiled into machine verifiable templates. BioInformatics Advances, 3(1-5):dx.doi.org/10.1093/bioadv/vbad068, 2023.

  5. Parsa Alan, Bharat Joshi, Ben Cardoen, Kurt Vandevoorde, Guang Gao, Peter Overby, James D. Johnson, Ghassan Hamarneh, and Ivan Robert Nabi. Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS (Alan, Joshi, Cardoen, and Vandevoorde: Joint first authors; Hamarneh and Nabi: Joint senior authors). Cellular and Molecular Life Sciences (CMLS), 79(565):1-20, 2022. 10.1007/s00018-022-04585-8, 2023.

  6. Ben Cardoen, Timothy H. Wong, Parsa Alan, Sieun Lee, Joanne Aiko Matsubara, Ivan Robert Nabi, and Ghassan Hamarneh. SPECHT: Self-tuning Plausibility Based Object Detection Enables Quantification of Conflict in Heterogeneous Multi-scale Microscopy (Nabi and Hamarneh: Joint senior authors). PLOS ONE, 17(12):e0276726, dx.doi.org/10.1371/journal.pone.0276726 2022.

  7. Hanene Ben Yedder, Ben Cardoen, and Ghassan Hamarneh. Deep Learning for Biomedical Image Reconstruction: A Survey. Artificial Intelligence Review (AIRE), 54(1):215-251, http://dx.doi.org/10.1007/s10462-020-09861-2 2021.

  8. Hanene Ben Yedder, Ben Cardoen, Majid Shokoufi, Farid Golnaraghi, and Ghassan Hamarneh. Multitask Deep Learning Reconstruction and Localization of Lesions in Limited Angle Diffuse Optical Tomography. IEEE Transactions on Medical Imaging (IEEE TMI), 41(3):515-530 https://doi.org/10.1109/TMI.2021.3117276, 2021.

  9. Ben Cardoen, Hanene Ben Yedder, Anmol Sharma, Keng C. Chou, Ivan Robert Nabi, and Ghassan Hamarneh. ERGO: Efficient Recurrent Graph Optimized Emitter Density Estimation in Single Molecule Localization Microscopy. IEEE Transactions on Medical Imaging (IEEE TMI), 39(6):1942-1956, http://dx.doi.org/10.1038/s41598-020-77170-3 2020.

  10. Rory Long, Kathleen Moriarty, Ben Cardoen, Guang Gao, A. Wayne Vogl, François Jean, Ghassan Hamarneh, and Ivan Robert Nabi. Super Resolution Microscopy and Deep Learning Identify Zika Virus Reorganization of the Endoplasmic Reticulum (Long and Moriarty: Joint first authors; Hamarneh and Nabi: Joint senior authors). Nature - Scientific reports, 10(20937):1-18, s41598-020-77170-32020.

  11. Cardoen Ben, Manhaeve S, Van Tendeloo Y, Broeckhove J. A PDEVS simulator supporting multiple synchronization protocols: implementation and performance analysis. SIMULATION. 2018;94(4):281-300. doi:10.1177/0037549717690826.

Conference #

  1. Ben Cardoen, Kurt Vandevoorde, Guang Gao, Milene Ortiz-Silva, Parsa Alan, Ellie Tiliakou, William Liu, A. Wayne Vogl, Ghassan Hamarneh, and Ivan Robert Nabi. Membrane contact site detection (MCS-DETECT) reveals dual control of rough mitochondria–ER contacts (Cardoen, Vandevoorde, Gao, and Ortiz: Joint first authors; Hamarneh and Nabi: Joint senior authors). In Keystone Symposia on Molecular and Cellular Biology - Organelle Membrane Contact Sites in Health and Disease (Joint with: Mitochondria Signaling and Disease), pages 1, 2024.

  2. Jieyi Zheng, Ben Cardoen, Ghassan Hamarneh, and Ivan Robert Nabi. Comparison of Specificity of Confocal and Super-Resolution Approaches to Detecting Mitochondria-ER Contact Sites (Hamarneh and Nabi: Joint senior authors). In Keystone Symposia on Molecular and Cellular Biology - Organelle Membrane Contact Sites in Health and Disease (Joint with: Mitochondria Signaling and Disease), pages 1, 2024.

  3. Parsa Alan, Bharat Joshi, Ben Cardoen, Kurt Vandevoorde, Guang Gao, Peter Overby, James D. Johnson, Ghassan Hamarneh, and Ivan Robert Nabi. Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS (Alan, Joshi, Cardoen, and Vandevoorde: Joint first authors; Hamarneh and Nabi: Joint senior authors). In American Society of Cell Biology (ASCB) - Cell Bio, 2022.

  4. Parsa Alan, Kurt Vandevoorde, Bharat Joshi, Ben Cardoen, Guang Goa, Ghassan Hamarneh, and Ivan Robert Nabi. Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS. In UBC SBME 2022, 2022.

  5. Ben Cardoen, Kurt Vandevoorde, Guang Gao, Parsa Alan, Ellie Tiliakou, William Liu, A. Wayne Vogl, Ghassan Hamarneh, and Ivan Robert Nabi. A novel sub-precision detection method (MCS-DETECT) identifies shape complexity of mitochondria-ER contacts (MERCs) in 3D STED super-resolution microscopy (Cardoen, Vandervoorde, and Gao: Joint first authors; Hamarneh and Nabi: Joint senior authors). In American Society of Cell Biology (ASCB) - Cell Bio, 2022.

  6. Ben Cardoen and Ghassan Hamarneh. Learning to look beyond what we can see: Leveraging statistical learning to improve scientific discovery from fluorescence microscopy. In Biomedical Imaging and Artificial Intelligence (BMIAI) cluster Fall Research Showcase, Vancouver, Canada, pages 1, 2021.

  7. Ben Cardoen, Timothy H. Wong, Parsa Alan, Sieun Lee, Joanne Aiko Matsubara, Ivan Robert Nabi, and Ghassan Hamarneh. Self-tuning Weakly Supervised Object Detection (SPECHT) of Sub-Diffraction Limited Caveolae and Scaffold and Amyloid-Beta Deposits. In American Society of Cell Biology – Cell Bio 2021, 2021.

  8. Ben Cardoen, Timothy H. Wong, Ivan Robert Nabi, and Ghassan Hamarneh. Belief theory enables detection of Caveolae in superresolution microscopy. In Microscopy Societies Symposium - Advanced Imaging and Analysis at Nanoscale, November 2021.

  9. Ben Cardoen, Timothy H. Wong, Parsa Alan, Sieun Lee, Joanne Aiko Matsubara, Ivan Robert Nabi, and Ghassan Hamarneh. Automatic identification of protein complexes in multi-scale microscopy with applications tometastasis and Alzheimer disease. In The 2nd Annual Tri-Cluster Research Day, Canada, pages 1, 2020.

  10. Ben Cardoen, Timothy H. Wong, Parsa Alan, Sieun Lee, Joanne Aiko Matsubara, Ivan Robert Nabi, and Ghassan Hamarneh. Belief theory enables identification of protein complexes in multi-scale microscopy with applications to metastasis and Alzheimer disease. In Centre for Artificial Intelligence Decision-making and Action (CAIDA), BC’s AI Showcase, Canada, pages 1, 2020.

  11. Ben Cardoen, Fiona Dickson, Ismail M. Khater, Ivan Robert Nabi, and Ghassan Hamarneh. Interaction zone analysis of CAV1 - CAVIN1 in breast cancer cells. In European Molecular Biology Organization EMBO Workshop Caveolae and nanodomains: Translating structural principles and dynamics into function, Le Pouliguen, France, pages 1, 2019.

  12. Hanene Ben Yedder, Ben Cardoen, Majid Shokoufi, Farid Golnaraghi, and Ghassan Hamarneh. Limited-Angle Diffuse Optical Tomography Image Reconstruction using Deep Learning. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11764, pages 66-74, 2019.

  13. Ben Cardoen, Stijn Manhaeve, Tim Tuijn, Yentl Van Tendeloo, Kurt Vanmechelen, Hans Vangheluwe, Jan Broeckhove. Performance analysis of a PDEVS simulator supporting multiple synchronization protocols In 2016 Symposium on Theory of Modeling and Simulation (TMS-DEVS)

Invited Talks #

  1. Ben Cardoen, Adversarial Attacks in Medical Imaging, UBC BMIAI Geering Up Outreach, 2020-11-20 doi/10.5281/zenodo.11943311

  2. Ben Cardoen, Ghassan Hamarneh Introduction to Causality, SFU MIAL/VCR Presentation, 2020-12-18 https://zenodo.org/doi/10.5281/zenodo.11953951

  3. Ben Cardoen, Wavelets: A gentle introduction for the wary researcher, SFU MIAL/VCR Presentation, 2021-11-25 doi/10.5281/zenodo.11948072

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