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Publications about 'Network Modelling and Analysis'
Articles in journal, book chapters
  1. Ismail M. Khater, Ivan Robert Nabi, and Ghassan Hamarneh. A Review of Super-resolution Single Molecule Localization Microscopy Cluster Analysis and Quantification Methods. Cell Patterns, 1(3):2666-3899, 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Deep Learning, Machine Learning, Classification, Graph based, Biomarkers/Biosignatures, Survey/Review. [bibtex-key = cellpatterns2020]


  2. Ismail M. Khater, Stephane Aroca-Ouellette, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Caveolae and scaffold detection from single molecule localization microscopy data using deep learning. PLOS ONE, 14(8):1-17, 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Deep Learning, Machine Learning, Classification, Graph based, Biomarkers/Biosignatures. [bibtex-key = plosone2019]


  3. Ismail M. Khater, Qian Liu, Keng C. Chou, Ghassan Hamarneh, and Ivan Robert Nabi. Super-resolution modularity analysis shows polyhedral caveolin-1 oligomers combine to form scaffolds and caveolae. Nature - Scientific reports, 9(9888):1-10, 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = nature_sr2019]


  4. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Identification of Caveolin-1 Domain Signatures via Graphlet Analysis of Single Molecule Super-Resolution Data. Bioinformatics, 35(18):3468-3475, 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning, Graphlets, Graph based, Biomarkers/Biosignatures. [bibtex-key = bioinformatics2019]


  5. Ismail M. Khater, Fanrui Meng, Timothy H. Wong, Ivan Robert Nabi, and Ghassan Hamarneh. Super Resolution Network Analysis Defines the Molecular Architecture of Caveolae and Caveolin-1 Scaffolds. Nature - Scientific reports, 8(9009):1-15, 2018. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = nature_sr2018]


Conference articles
  1. Ismail M. Khater, Ivan Robert Nabi, and Ghassan Hamarneh. HDCluster: High-Degree Graph-Based Clustering Algorithm and its Application to Single Molecule Localization Microscopy. In Single Molecule Localization Microscopy Symposium, pages 1, 2022. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Clustering. [bibtex-key = smlms2022]


  2. Ismail M. Khater, Timothy H. Wong, Christian Hallgrimson, Satish Moparthi, Stéphane Vassilopoulos, Ghassan Hamarneh, and Ivan Robert Nabi. Molecular architecture of clathrin plaques and pits defined by super-resolution network analysis (SuperResNET) (Khater and Wong: Joint first authors; Hamarneh and Nabi: Joint senior authors). In American Society of Cell Biology (ASCB) - Cell Bio, 2022. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Software and Tools, Network Modelling and Analysis, Machine Learning. [bibtex-key = ascb2022b]


  3. Ismail M. Khater, Timothy H. Wong, Stéphane Vassilopoulos, Ivan Robert Nabi, and Ghassan Hamarneh. SuperResNET: a GUI software package for single molecule localization microscopy cluster analysis (Nabi and Hamarneh: Joint senior authors). In Single Molecule Localization Microscopy Symposium - Current Trends, pages 1, 2021. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Software and Tools, Network Modelling and Analysis, Machine Learning. [bibtex-key = smlms2021]


  4. Ismail M. Khater, Ivan Robert Nabi, and Ghassan Hamarneh. SuperNet: Super-resolution Network Analysis and Quantification of Single Molecule Clusters. In Single Molecule Localization Microscopy Symposium - Showtime, pages 1, 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Software and Tools, Network Modelling and Analysis, Machine Learning. [bibtex-key = smlms2020]


  5. Ismail M. Khater, Ivan Robert Nabi, and Ghassan Hamarneh. Identification of Cav1 Domains Using Super Resolution Microscopy and Machine Learning. In European Molecular Biology Organization EMBO Workshop Caveolae and nanodomains: Translating structural principles and dynamics into function, Le Pouliguen, France, pages 1, 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = embo2019b]


  6. Timothy H. Wong, Mona Shahsavari, Ismail M. Khater, Bharat Joshi, Ghassan Hamarneh, and Ivan Robert Nabi. Super Resolution Microscopy Identification of Focal Adhesion-Associated Caveolin-1 Domains (Wong and Shahsavari: Joint first authors). In European Molecular Biology Organization EMBO Workshop Caveolae and nanodomains: Translating structural principles and dynamics into function, Le Pouliguen, France, pages 1, 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis. [bibtex-key = embo2019c]


  7. Ismail M. Khater, Qian Liu, Keng C. Chou, Ghassan Hamarneh, and Ivan Robert Nabi. Modular Structure of Caveolin-1 Scaffolds and Caveolae Identified by Single Molecule Localization Microscopy. In American Society for Cell Biology and European Molecular Biology Organization (ASCB-EMBO), San Diego, USA, pages 1343 (Abstract P2707), 2018. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning, Graph based. [bibtex-key = ascb2018b]


  8. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Caveolin-1 Domain Characterization Using Machine Learning and Graphlet Analysis of Single Molecule Super Resolution Microscopy. In American Society for Cell Biology and European Molecular Biology Organization (ASCB-EMBO), San Diego, USA, pages 1342 (Abstract P2706), 2018. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning, Graphlets, Graph based, Biomarkers/Biosignatures. [bibtex-key = ascb2018a]


  9. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Characterization of caveolin-1 domains via graphlet decomposition of SMLM super resolution data. In Genesis BME day, Vancouver, Canada, pages 1, 2018. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning, Graphlets, Graph based, Biomarkers/Biosignatures. [bibtex-key = bme2018]


  10. Ismail M. Khater, Youtao Liu, Qian Liu, Fanrui Meng, Keng C. Chou, Ivan Robert Nabi, and Ghassan Hamarneh. Distinguishing Biological and Non-Biological Networks in Single Molecule Localization Super Resolution Microscopy. In American Society for Cell Biology and European Molecular Biology Organization (ASCB-EMBO), Philadelphia, USA, pages 1, 2017. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = ascb2017]


  11. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Filtering, Segmenting, and Quantifying Caveolin-1 Protein Clusters in 3D Super-Resolution Microscopy via Machine-Learning and Network Analysis. In 2nd Annual Health Technology Symposium, Vancouver, Canada, pages 1, 2017. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = healthtech2017d]


  12. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Filtering, Segmenting, and Quantifying Caveolin-1 Protein Clusters in 3D Super-Resolution Microscopy via Machine-Learning and Network Analysis. In SIAM-IMAGING Manitoba Workshop on Mathematical Imaging Science, Winnipeg, Canada, pages 1, 2017. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = siam2017a]


  13. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Filtering, Segmenting, and Quantifying Caveolin-1 Protein Clusters in 3D Super-Resolution Microscopy via Machine-Learning and Network Analysis. In Gordon Research Conference, Andover, NH, USA, pages 1, 2017. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = gordon2017a]


  14. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Molecular Level Quantification of Cav1 Clusters in Super-Resolution Imaging Data. In Frontiers in Biophysics, Vancouver, Canada, pages 1, 2017. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = frontiers_biophysics2017]


  15. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Defining caveolae and scaffolds by computational network analysis of particle localization super-resolution microscopy. In American Society for Cell Biology (ASCB), San Francisco, California, pages 1, 2016. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = ascb2016]


  16. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Discovering Biosignatures of Cav1 Domains: Computational Methods for Super-resolution Microscopy. In LSI Imaging Super-resolution Mini-symposium, Vancouver, Canada, pages 1, 2016. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = superres2016]


  17. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Quantifying Caveolin-1 Molecular Domains via Machine Learning and Computational Network Analysis of Super-resolution Microscopy Data. In Bringing the ASCB to the LSI Imaging Mini-symposium, Vancouver, Canada, pages 1, 2016. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = ascblsi2016]


  18. Ismail M. Khater, David Scriven, Edwin Moore, and Ghassan Hamarneh. Sub-Cellular Network Analysis of Ryanodine Receptor Positioning in Control and Phosphorylated States. In IEEE Computing in Cardiology (IEEE CinC), pages 821-824, 2016. Keyword(s): Cardiology, Super Resolution Microscopy, Single Molecule Localization, Network Modelling and Analysis. [bibtex-key = cinc2016]


  19. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Identifying Sub-Cellular Domains in PC3 cells by Analysing Caveolin-1 Proteins from Nanoscopy Super-Resolution Data. In NanoLytica, Burnaby, Canada, pages 1, 2015. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = nanolytica2015]


  20. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Super-resolution analysis of Caveolae and Cav1 scaffolds in Prostate Cancer Cells. In Advanced Structural and Chemical Imaging (ASCI) Symposium, Pullman, Washington, pages 1, 2015. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = asci2015]


  21. Fanrui Meng, Ismail M. Khater, Ghassan Hamarneh, and Ivan Robert Nabi. Super-resolution analysis of Caveolae and Cav1 scaffolds in Prostate Cancer Cells. In Canadian Cytometry and Microscopy Association (CCMA), Toronto, Canada, pages 1, 2015. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = ccma2015]


Internal reports
  1. Ashwin Samudre, Guang Gao, Ben Cardoen, Ivan Robert Nabi, and Ghassan Hamarneh. nERdy: network analysis of endoplasmic reticulum (Nabi and Hamarneh: Joint senior authors). Technical report biorxiv:2024.02.20.581259, 2 2024. Keyword(s): Super Resolution Microscopy, Software and Tools, Network Modelling and Analysis, Machine Learning, Deep Learning, Anatomical Trees and Tubular Structures, Synthesis/Simulation/Augmentation. [bibtex-key = biorxiv_2024_02_20_581259]


  2. Ismail M. Khater, Stephane Aroca-Ouellette, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Caveolae and scaffold detection from single molecule localization microscopy data using deep learning. Technical report biorxiv:495382, 1 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Deep Learning, Network Modelling and Analysis, Machine Learning. [bibtex-key = biorxiv_2019_526327]


  3. Ismail M. Khater, Qian Liu, Keng C. Chou, Ghassan Hamarneh, and Ivan Robert Nabi. Super-resolution modularity analysis shows that polyhedral caveolin-1 oligomers combine to form scaffolds and caveolae. Technical report biorxiv:495382, 12 2018. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = biorxiv_2018_495382]



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Last modified: Wed Mar 27 16:05:03 2024
Author: hamarneh.


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