**Journal Articles**

- Mohammad Wasih, Sahil Ahmad and Mohamed K. Almekkawy, 2023, "A robust cascaded deep neural network for image reconstruction of single plane wave ultrasound RF data", Ultrasonics,
**132**, pp. 106981

- Xilun Liu and Mohamed K. Almekkawy, 2023, "Ultrasound Localization Microscopy Using Deep Neural Network", IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control,
**70**, (7), pp. 625-635

- Anita Carevic, Ivan Slapnicar and Mohamed Almekkawy, 2022, "Solving Ultrasound Tomography’s Inverse Problem: Automating Regularization Parameter Selection", IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control,
**69**, (8), pp. 2447-2461

- S Prasad and Mohamed K. Almekkawy, 2022, "DeepUCT: Complex cascaded deep learning network for improved ultrasound tomography", Physics in Medicine & Biology,
**67**, (6), pp. 065008

- Skanda Bharadwaj, Sumukha Prasad and Mohamed K. Almekkawy, 2021, "An Upgraded Siamese Neural Network for Motion Tracking in Ultrasound Image Sequences", IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control,
**68**, (12), pp. 3515-3527

- Qinhan Gao and Mohamed K. Almekkawy, 2021, "ASU-Net++: A nested U-Net with adaptive feature extractions for liver tumor segmentation", Computers in Biology and Medicine,
**136**, pp. 104688

- Umar Farooq Mohammmad and Mohamed K. Almekkawy, 2021, "Automated detection of liver steatosis in ultrasound images using convolutional neural networks", The Journal of the Acoustical Society of America,
**149**, (4), pp. A114-A115

- Anita Carevic, Ivan Slapnicar and Mohamed K. Almekkawy, 2021, "Automated regularization parameters method for the inverse problem in ultrasound tomography", The Journal of the Acoustical Society of America,
**149**, (4), pp. A42-A42

- Skanda Bharadwaj and Mohamed K. Almekkawy, 2021, "Improved Siamese Network for motion tracking in ultrasound images", The Journal of the Acoustical Society of America,
**149**, (4), pp. A114-A114

- Qinhan Gao and Mohamed K. Almekkawy, 2021, "Ultrasound liver tumor segmentation with nested U-Net and dynamic feature extraction", The Journal of the Acoustical Society of America,
**149**, (4), pp. A115-A115

- Umar Farooq Mohammmad, Mohammad Wasih and Mohamed K. Almekkawy, 2021, "A substitution of convolutional layers by FFT layers—A low computational cost version", The Journal of the Acoustical Society of America,
**149**, (4), pp. A114-A114

- Brandon Rebholz, Fei Zheng and Mohamed K. Almekkawy, 2020, "Two-dimensional iterative projection method for subsample speckle tracking of ultrasound images", Medical & Biological Engineering & Computing,
**58**, (12), pp. 2937-2951

- Sumukha Prasad and Mohamed K. Almekkawy, 2020, "A fast and efficient ultrasound tomography using deep learning", The Journal of the Acoustical Society of America,
**148**, (4), pp. 2450-2450

- Skanda Bharadwaj and Mohamed K. Almekkawy, 2020, "Motion estimation for ultrasound image sequences using deep learning", The Journal of the Acoustical Society of America,
**148**, (4), pp. 2487-2487

- Niranjan Thirusangu, Thyagarajan Subramanian and Mohamed K. Almekkawy, 2020, "Segmentation of induced substantia nigra from transcranial ultrasound images using deep convolutional neural network", The Journal of the Acoustical Society of America,
**148**, (4), pp. 2636-2637

- Mohamed K. Almekkawy, Anita Carevic, Ahmed Abdou, Jiayu He, Geunseop Lee and Jesse L Barlow, 2020, "Regularization in ultrasound tomography using projection-based regularized total least squares", Inverse Problems in Science and Engineering,
**28**, (4), pp. 556-579

- Xilun Liu and Mohamed K. Almekkawy, 2020, "An Optimized Control approach for HIFU Tissue Ablation Using PDE Constrained Optimization Method", IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, pp. 1-1

- Daniel McMahon and Mohamed K. Almekkawy, 2020, "Elements Selection for Transcostal HIFU Refocusing Method: Simulation Study", IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, pp. 1-1

- Mohamed K. Almekkawy and E. Ebbini, 2019, "The Optimization of Transcostal Phased Array Refocusing Using the Semidefinite Relaxation Method", IEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control

- Mohamed K. Almekkawy, J. Chen, M. Ellis, D. Haemmerich, D. Holmes, C. Linte, D. Panescu, J. Pearce, P. Prakash and V. Zderic, 2019, "Therapeutic Systems and Technologies: State-of-the-Art, Applications, Opportunities and Challenges."

- I.A. Shehata Elhelf, H. Albahar, U. Shah, A. Oto, E. Cressman and Mohamed Almekkawy, 2018, "High intensity focused ultrasound: The fundamentals, clinical applications and research trends", Diagnostic and Interventional Imaging,
**99**, (6), pp. 349-359

- Jingwei Xu, Yi Zheng, Mohan Chirala and Mohamed Almekkaway, 2018, "An FPGA Implementation of Resource-Optimized Dynamic Digital Beamformer for a Portable Ultrasound Imaging System", Advances in Science, Technology and Engineering Systems Journal,
**3**, (4), pp. 59-71

- Mohamed K. Almekkaway, Islam A. Shehata and Emad S. Ebbini, 2015, "Anatomical-based model for simulation of HIFU-induced lesions in atherosclerotic plaques", International Journal of Hyperthermia,
**31**, (4), pp. 433-442

- Mohamed K. Almekkawy, 2015, "Anatomical-based model for simulation of HIFU-induced lesions in atherosclerotic plaques", International Journal of Hyperthermia,
**31**, (4), pp. 433-442

- Mohamed K. Almekkawy, Yasaman Adibi, Fei Zheng, Mohan Chirala and Emad S. Ebbini, 2014, "Two-dimensional speckle tracking using zero phase crossing with Riesz transform", The Journal of the Acoustical Society of America,
**136**, (4), pp. 2280-2280

- A. Singal, A. Hamel, M. Larson, H. Kelner, Mohamed K. Almekkawy, Mohamed K. Almekkawy and P. Eckman, 2014, "Peripheral Pulse Wave Analysis Technique to Detect Aortic Valve State in Continuous-flow LVADs", The Journal of Heart and Lung Transplantation,
**33**, (4), pp. S75

- Ashish Singal, Mitsuhiro Oura, Mohamed K. Almekkawy, Aimee Hamel, Matt Larson and Peter Eckman, 2013, "Device Optimization Using Pulse Wave Analysis Techniques", Journal of Medical Devices,
**7**, (2), pp. 020903

- Mohammad Wasih, Sahil Ahmad and Mohamed Almekkawy, , "A Robust Cascaded Deep Neural Network for Image Enhancement of Single Plane Wave Ultrasound RF Data", SSRN Electronic Journal

- Ahmed AL Qurri and Mohamed K. Almekkawy, , "Improved UNet with Attention for Medical Image Segmentation", Sensors,
**23**, (20), pp. 8589

- Shaikhah Alkhadhr and Mohamed K. Almekkawy, , "Wave Equation Modeling via Physics-Informed Neural Networks: Models of Soft and Hard Constraints for Initial and Boundary Conditions", Sensors,
**23**, (5), pp. 2792

**Conference Proceedings**

- Qinhan Gao and Mohamed K. Almekkawy, 2023, "Deep Learning based Ultrasound Computed Tomography for Real-Time Construction", IEEE

- Mohammed S. Alshahrani, Mohammad Wasih and Mohamed K. Almekkawy, 2023, "Imposing Object’s Trajectory and Dynamic Template Updates to Track ROIs in Ultrasound Image Sequences", IEEE

- Shaikhah Alkhadhr and Mohamed K. Almekkawy, 2023, "Modeling a Multi-Element Ultrasound Transducer via Component-Focused Physics-informed Neural Networks", IEEE

- Xilun Liu and Mohamed K. Almekkawy, 2023, "Ultrasound Microbubbles Localization Using Object Detection Model", IEEE

- Shaikhah Alkhadhr and Mohamed K. Almekkawy, 2023, "Modeling the Wave Equation Using Physics-Informed Neural Networks Enhanced With Attention to Loss Weights", IEEE

- Xilun Liu and Mohamed K. Almekkawy, 2023, "Full Wave Inversion For Ultrasound Tomography Using Physics Based Deep Neural Network", IEEE

- Xilun Liu and Mohamed K. Almekkawy, 2023, "Ultrasound Super Resolution Using Deep Learning Based on Attention Mechanism", IEEE

- Mohammad Wasih and Mohamed Almekkawy, 2022, "A Robust Deep Neural Network Approach for Ultrafast Ultrasound Imaging using Single Angle Plane Wave", IEEE

- Anita Carevic, Ivan Slapnicar and Mohamed Almekkawy, 2022, "Automating Regularization Parameter Selection of the Inverse Problem in Ultrasound Tomography", IEEE

- Shaikhah Alkhadhr and Mohamed Almekkawy, 2022, "Physics-Informed Neural Networks with Resampling Technique to Model Ultrasound Wave Propagation of a Multi-Element Transducer", IEEE

- Xilun Liu and Mohamed Almekkawy, 2022, "Ultrasound Super Resolution using Vision Transformer with Convolution Projection Operation", IEEE

- Mohammad Wasih and Mohamed Almekkawy, 2022, "Analysis of Advanced Siamese Neural Networks for Motion Tracking of Sonography of Carotid Arteries", IEEE

- Sumukha Prasad and Mohamed Almekkawy, 2022, "DL-UCT: A Deep Learning Framework for Ultrasound Computed Tomography", IEEE

- Shaikhah Alkhadhr and Mohamed K. Almekkawy, 2021, "A Combination of Deep Neural Networks and Physics to Solve the Inverse Problem of Burger’s Equation", IEEE

- Mohammad Wasih and Mohamed K. Almekkawy, 2021, "A Novel Deep Learning Approach for Tracking Regions of Interest in Ultrasound Images*", IEEE

- Aishwarya Mallampati and Mohamed K. Almekkawy, 2021, "Measuring Tissue Elastic Properties Using Physics Based Neural Networks", IEEE

- Niranjan Thirusangu and Mohamed K. Almekkawy, 2021, "Segmentation of Breast Ultrasound Images using Densely Connected Deep Convolutional Neural Network and Attention Gates", IEEE

- Yuzhang Wang and Mohamed K. Almekkawy, 2021, "Simulation of Temperature Distribution During HIFU Therapy Using Physics Based Deep Learning Method", IEEE

- Xilun Liu and Mohamed K. Almekkawy, 2021, "Temperature Control of the Focal Point of Focused Ultrasound Excitation Using Neural Network Approach", IEEE

- Xilun Liu and Mohamed K. Almekkawy, 2021, "Ultrasound Computed Tomography using physical-informed Neural Network", IEEE

- Shaikhah Alkhadhr, Xilun Liu and Mohamed K. Almekkawy, 2021, "Modeling of the Forward Wave Propagation Using Physics-Informed Neural Networks", IEEE

- Shaikhah Alkhadhr and Mohamed K. Almekkawy, 2021, "Modeling of the Wave Propagation of a Multi-Element Ultrasound Transducer Using Neural Networks", IEEE

- Mohammad Wasih and Mohamed K. Almekkawy, 2021, "Motion Tracking of Carotid Artery in Ultrasound Images Using Lucas Kanade Method with Advanced Siamese Neural Networks", IEEE

- Yuzhang Wang, Shaikhah Alkhadhr and Mohamed K. Almekkawy, 2021, "PINN Simulation of the Temperature Rise Due to Ultrasound Wave Propagation", IEEE

- Umar Farooq Mohammad and Mohamed K. Almekkawy, 2021, "A Substitution of Convolutional Layers by FFT Layers - A Low Computational Cost Version", IEEE

- Mohammad Wasih and Mohamed K. Almekkawy, 2021, "Advanced Deep Learning Network with Harris Corner based Background Motion Modeling for Motion Tracking of Targets in Ultrasound Images", IEEE

- Umar Farooq Mohammad and Mohamed K. Almekkawy, 2021, "Automated Detection of Liver Steatosis in Ultrasound Images Using Convolutional Neural Networks", IEEE

- Brandon Rebholz and Mohamed K. Almekkawy, 2020, "Analysis of Speckle Tracking Methods: Correlation and RF Interpolation", IEEE

- Michael S. Maslakowski, Sheikh J. Ilham, Timothy Hall, Thyagarajan Subramanian, Mehdi Kiani and Mohamed K. Almekkawy, 2020, "The Characterization and Assembly of an Efficient, Cost Effective Focused Ultrasound Transducer", IEEE

- Brandon Rebholz and Mohamed K. Almekkawy, 2020, "Constrained RF Level Interpolation for Normalized Cross Correlation Based Speckle Tracking", IEEE

- Skanda Bharadwaj and Mohamed K. Almekkawy, 2020, "Deep Learning Based Motion Tracking of Ultrasound Image Sequences", IEEE

- Brandon Rebholz and Mohamed K. Almekkawy, 2020, "Efficacy Of Kriging Interpolation In Ultrasound Imaging; Subsample Displacement Estimation", IEEE

- Skanda Bharadwaj and Mohamed K. Almekkawy, 2020, "Faster Search Algorithm for Speckle Tracking in Ultrasound Images", IEEE

- Carevi\'c, Anita, Xingzhao Yun and Mohamed K. Almekkawy, 2019, "Adaptive truncated total least square on distorted born iterative method in ultrasound inverse scattering problem",
**10955**, pp. 1095515

- Carevi\'c, Anita, Ahmed Abdou, Slapni\vcar, Ivan and Mohamed K. Almekkawy, 2019, "Employing methods with generalized singular value decomposition for regularization in ultrasound tomography",
**10955**, pp. 1095509

- James Cunningham, Yi Zheng, Thyagarajan Subramanian and Mohamed Almekkawy, 2018, "Improved Real-Time Capability for Nonlinear Seperable Harmonic Filtering of Ultrasound Images Using a Damped Regularization Method With In-Vivo Results", IEEE

- Poojitha Kale, J. Vinita Acharya, Jayant Acharya, Thyagarajan Subramanian and Mohammed Almekkawy, 2018, "Normalized Transfer Entropy as a Tool to Identify Multisource Functional Epileptic Networks", IEEE

- Anita Carevic, Ali E. Abdou, Jesse L Barlow and Mohamed Almekkawy, 2018, "Using Filter Factors for Regularization in Ultrasound Tomography", IEEE

- James Cunningham, Yi Zheng, Thyagarajan Subramanian and Mohamed Almekkawy, 2018, "Regularization methods for solving third-order volterra filter with improved convergence speed: In-vivo application", IEEE

- Mohamed Almekkawy, Anita Carevic, Xingzhao Yun, Ivan Slapnicar, Ali Abdou, Geunseop Lee and Jesse L Barlow, 2018, "Solving the ultrasound inverse scattering problem of inhomogeneous media using different approaches of total least squares algorithms", SPIE

- A. Carevic, X. Yun, G. Lee, I. Slapnicar, Jesse L Barlow and Mohamed K. Almekkawy, 2018, "Reconstruction of ultrasound tomography for cancer detection using total least squares and conjugate gradient method"

- P. Kale, T. Gilmour, V. Acharya, J. Acharya, T. Subramanian and Mohamed K. Almekkawy, 2017, "Prediction of Multifocal Epileptogenic Zones using Normalized Transfer Entropy"

- J. Cunningham, T. Subramanian and Mohamed K. Almekkawy, 2017, "Adaptive l 0-norm Sparse Third Order Volterra Filter for Transcranial Ultrasound Image Enhancement: In-Vivo Results"

- A. Lee, Mohamed K. Almekkawy, P. Kale, T. Gilmour, T. Subramanian, M. Sather, V. Acharya and J. Acharya, 2017, "Can normalized transfer entropy be used as an informational transfer measure of ictal pathophysiology in patients undergoing stereo-EEG for epilepsy surgery", American Epilepsy Society

- Mohamed K. Almekkawy, Daniel McMahon, Hanan Alqarni and Jiayu He, 2017, "Optimization of Transcostal Phased-array Refocusing Using Sparse Semidefinite Relaxation Method", IEEE Engineering in Medicine and Biology Society, pp. 1449-1452

- Mohamed K. Almekkawy, James Cunningham, Yi Song, Hadeel Albahar and Thyagarajan Subramanian, 2017, "In-vivo transcranial ultrasound imaging of induced Substantia Nigra hyperechogenicity using adaptive sparse Third Order Volterra Filter", IEEE, pp. 367-370

- James Cunningham, Justice Lee, Thyagarajan Subramanian and Mohamed K. Almekkawy, 2017, "Transcranial enhanced Ultrasound Imaging of induced substantia nigra in brain using adaptive Third Order Volterra Filter: In-vivo results", IEEE, pp. 684-687

- Mohamed K. Almekkawy and Emad Ebbini, 2017, "Two-dimensional speckle tracking using parabolic polynomial expansion with Riesz transform", IEEE, pp. 201-205

- Mohamed K. Almekkawy, I. A. Shehata, A. Haritonova, J. Ballard, A. Casper and E. Ebbini, 2017, "Image-based numerical modeling of HIFU-induced lesions",
**1816**, (1)

- J. Cunningham, Y. Zheng, T. Subramanian and Mohamed K. Almekkawy, 2017, "Regularization Methods for Solving Third-Order Volterra Filter with Improved Convergence Speed: In-Vivo Application"

- A. Carevic, X. Yun, G. Lee, I. Slapnicar, Jesse L Barlow and Mohamed K. Almekkawy, 2017, "Solving the ultrasound inverse scattering problem of inhomogeneous media using different approaches of total least squares algorithms"

- Mohamed K. Almekkaway, Islam A. Shehata, Alyona Haritonova, John Ballard, Andrew Casper and Emad Ebbini, 2017, "Image-based numerical modeling of HIFU-induced lesions", Author(s)

- Admir Horta, Eric Gernux, Matt Couceiro, Dieter Haemmerich and Mohamed K. Almekkawy, 2016, "Body temperature control circuit", IEEE

- Mohamed K. Almekkawy, Jingwei Xu and Mohan Chirala, 2014, "An optimized ultrasound digital beamformer with dynamic focusing implemented on FPGA", IEEE

- Mohamed K. Almekkawy, J. R. Ballard, D. Liu, A. J. Casper, Y. Wan and E. Ebbini, 2012, "Multiple-frequency phased array patterns for therapeutic ultrasound",
**1481**, (1), pp. 9-13

- Mohamed K. Almekkawy, A. Casper, J. Ballard and E. Ebbini, 2012, "Nonlinear modeling of pulsed and CW HIFU beams for dual-mode ultrasound arrays",
**1481**, (1), pp. 3-8

- J. R. Ballard, D. Liu, Mohamed K. Almekkawy, E. S. Ebbini, A. Casper and A. Haritonova, 2011, "Multiple-frequency phased array pattern synthesis for HIFU surgery"

- Mohamed K. Almekkawy, A. M. Mahmoud, A. Zavochikove and A. E. Salama, 2005, "Reliable design of the CAN bit synchronization block"

- Sumukha Prasad and Mohamed K. Almekkawy, , "DL-UCT: A Deep Learning Framework for Ultrasound Computed Tomography",
*IEEE International Symposium on Biomedical Imaging*

**Abstracts**

- I Shehata, H Abdelaal, A Almekkawy, H Albahar and Mohamed K. Almekkawy, 2018, "The Emerging Role of high intensity focused ultrasound (HIFU) in cancer Immunomodulation"

- Jesse L Barlow, A Carevic, X Yun, I Slapnicar and Mohamed K. Almekkawy, 2018, "Adaptive Truncated Total Least Squares for an Inverse Scattering Problem from Ultrasound Tomography"

- Rebholz and Mohamed K. Almekkawy, 2018, "Multidimensional Motion Estimation with Stochastic Interpolation via Disjunctive Kriging,"

- A Carevic, Jesse L Barlow and Mohamed K. Almekkawy, 2018, "Projection Based Total Least Square Algorithm for Ultrasound Tomography"

- A Carevic, Jesse L Barlow, I Slapnicar and Mohamed K. Almekkawy, 2018, "Regularization of Inverse Scattering Problem in Ultrasound Tomography"

- D. McMahon and Mohamed K. Almekkawy, 2017, "Optimization of Transcostal Phased-array Refocusing Using Iterative Sparse Semidefinite Relaxation Method"

- A. Lee, Mohamed K. Almekkawy, P. Kale, T. Gilmour, T. Subramanian, M. Sather, V. Acharya and J. Acharya, 2017, "Can Normalized Transfer Entropy Be Used as an Informational Transfer Measure of Ictal Pathophysiology in Patients Undergoing Stereo-EEG for Epilepsy Surgery?"

- Jesse L Barlow, A. Carevic, X. Yun and Mohamed K. Almekkawy, 2017, "Adaptive Truncated Total Least Squares for an Inverse Scattering Problem from Ultrasound Tomography"

- Mohamed K. Almekkawy, I. Shehata, A. Casper, J. Ballard, M. Troutman and E. Ebbini, 2012, "Modeling Thermal Lesion Formation in Atheromatous Plaque Tissue using high intensity focused ultrasound (HIFU): comparison within vivo results"