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). The Journal Of Cell Biology (JCB), 1(jcb.202206109):000-000, 11 2023. Keyword(s): Super Resolution Microscopy, Object Detection, Restoration, Reconstruction, Interaction. [bibtex-key = jcb2023]



2. 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. Keyword(s): Super Resolution Microscopy, Image Processing, Belief Theory. [bibtex-key = cmls2022]



3. 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, 2022. Keyword(s): Super Resolution Microscopy, Machine Learning, Classification, Belief Theory, Biomarkers/Biosignatures, Generalizability. [bibtex-key = plosone2022]

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. Keyword(s): Super Resolution Microscopy, Object Detection, Restoration, Reconstruction, Interaction. [bibtex-key = ksmcb2024a]



2. 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. Keyword(s): Super Resolution Microscopy, Image Processing, Belief Theory. [bibtex-key = ascb2022c]



3. 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. Keyword(s): Super Resolution Microscopy, Image Processing, Belief Theory. [bibtex-key = sbme2022]



4. 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. Keyword(s): Object Detection, Super Resolution Microscopy. [bibtex-key = ascb2022a]



5. 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. Keyword(s): Object Detection, Super Resolution Microscopy, Belief Theory, Datasets. [bibtex-key = cellbio2021]



6. 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. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Processing, Belief Theory. [bibtex-key = tricluster2020b]



7. 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. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Processing, Belief Theory. [bibtex-key = caida2020b]

1. Parsa Alan, Kurt Vandevoorde, Bharat Joshi, Ben Cardoen, Guang Gao, Yahya Mohammadzadeh, Ghassan Hamarneh, and Ivan Robert Nabi. Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS (Alan, Vandevoorde, Joshi, and Cardoen: Joint first authors; Hamarneh and Nabi: Joint senior authors). Technical report Research Square (Preprint) 1559637, 4 2022. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Deep Learning, Image Processing, Belief Theory. [bibtex-key = research_square2022_1559637]



2. Ben Cardoen, Guang Gao, Kurt Vandevoorde, Parsa Alan, William Liu, Ghassan Hamarneh, and Ivan Robert Nabi. Automatic sub-precision membrane contact site detection identifies convoluted tubular riboMERCs (Cardoen, Gao, Vandevoorde: Joint first authors; Hamarneh and Nabi: Joint senior authors). Technical report biorxiv:2022.06.23.497346, 6 2022. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Color/Multichannel/Vector-valued, Image Reconstruction. [bibtex-key = biorxiv_2022_06_23_497346]



3. Parsa Alan, Bharat Joshi, Ben Cardoen, Kurt Vandevoorde, Guang Gao, Yahya Mohammadzadeh, Ghassan Hamarneh, and Ivan Robert Nabi. Gp78-mediated basal mitophagy promotes mitochondrial health and limits mitochondrial ROS production (Alan, Joshi, Cardoen, and Vandevoorde: Joint first authors; Hamarneh and Nabi: Joint senior authors). Technical report biorxiv:2021.09.17.460825, 9 2021. Keyword(s): Super Resolution Microscopy, Image Processing, Belief Theory. [bibtex-key = biorxiv_2021_09_17_460825]



4. 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). Technical report techrxiv:12971051, 9 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Processing, Belief Theory, Object Detection, Datasets. [bibtex-key = techrxiv_12971051]

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