Fast nonrigid image registration using statistical deformation models learned from richly-annotated data. - John A. Onofrey; Lawrence H. Staib; Xenophon Papademetris (ISBI, 2013)

Learning Nonrigid Deformations for Constrained Multi-modal Image Registration. - John A. Onofrey; Lawrence H. Staib; Xenophon Papademetris (MICCAI (3), 2013)

Semi-supervised Learning of Nonrigid Deformations for Image Registration. - John A. Onofrey; Lawrence H. Staib; Xenophon Papademetris (MCV, 2013)

A Scalable Algorithm for Structured Kernel Feature Selection. - Shaogang Ren; Shuai Huang 001; John A. Onofrey; Xenios Papademetris; Xiaoning Qian (AISTATS, 2015)

Segmenting the Brain Surface from CT Images with Artifacts Using Dictionary Learning for Non-rigid MR-CT Registration. - John A. Onofrey; Lawrence H. Staib; Xenophon Papademetris (IPMI, 2015)

Learning nonrigid deformations for constrained point-based registration for image-guided MR-TRUS prostate intervention. - John A. Onofrey; Lawrence H. Staib; Saradwata Sarkar; Rajesh Venkataraman; Xenophon Papademetris (ISBI, 2015)

Low-Dimensional Non-Rigid Image Registration Using Statistical Deformation Models From Semi-Supervised Training Data. - John A. Onofrey; Xenophon Papademetris; Lawrence H. Staib (IEEE Trans. Medical Imaging, 2015)

MRI-TRUS Image Synthesis with Application to Image-Guided Prostate Intervention. - John A. Onofrey; Ilkay Öksüz; Saradwata Sarkar; Rajesh Venkataraman; Lawrence H. Staib; Xenophon Papademetris (SASHIMI@MICCAI, 2016)

Learning Non-rigid Deformations for Robust, Constrained Point-based Registration in Image-Guided MR-TRUS Prostate Intervention. - John A. Onofrey; Lawrence H. Staib; Saradwata Sarkar; Rajesh Venkataraman; Cayce B. Nawaf; Preston C. Sprenkle; Xenophon Papademetris (Medical Image Anal., 2017)

A fetal fMRI specific motion correction algorithm using 2nd order edge features. - Dustin Scheinost; John A. Onofrey; Soo Hyun Kwon; Sarah N. Cross; Gordon Sze; Laura R. Ment; Xenophon Papademetris (ISBI, 2018)

Better Feature Matching for Placental Panorama Construction. - Praneeth Sadda; John A. Onofrey; Mert Ozan Bahtiyar; Xenophon Papademetris (DATRA/PIPPI@MICCAI, 2018)

Deep Learning Retinal Vessel Segmentation from a Single Annotated Example: An Application of Cyclic Generative Adversarial Neural Networks. - Praneeth Sadda; John A. Onofrey; Xenophon Papademetris (CVII-STENT/LABELS@MICCAI, 2018)

Non-Rigid Event-by-Event Continuous Respiratory Motion Compensated List-Mode Reconstruction for PET. - Chung Chan; John A. Onofrey; Yiqiang Jian; Mary Germino; Xenophon Papademetris; Richard E. Carson; Chi Liu 001 (IEEE Trans. Medical Imaging, 2018)

Generalizable Multi-Site Training and Testing Of Deep Neural Networks Using Image Normalization. - John A. Onofrey; Dana I. Casetti-Dinescu; Andreas D. Lauritzen; Saradwata Sarkar; Rajesh Venkataraman; Richard E. Fan; Geoffrey A. Sonn; Preston C. Sprenkle; Lawrence H. Staib; Xenophon Papademetris (ISBI, 2019)

A Novel Loss Function Incorporating Imaging Acquisition Physics for PET Attenuation Map Generation Using Deep Learning. - Luyao Shi; John A. Onofrey; Enette Mae Revilla; Takuya Toyonaga; David Menard; Joseph Ankrah; Richard E. Carson; Chi Liu 001; Yihuan Lu (MICCAI (4), 2019)

Deep-learned placental vessel segmentation for intraoperative video enhancement in fetoscopic surgery. - Praneeth Sadda; Metehan Imamoglu; Michael Dombrowski; Xenophon Papademetris; Mert Ozan Bahtiyar; John A. Onofrey (Int. J. Comput. Assist. Radiol. Surg., 2019)

Segmenting the Brain Surface From CT Images With Artifacts Using Locally Oriented Appearance and Dictionary Learning. - John A. Onofrey; Lawrence H. Staib; Xenophon Papademetris (IEEE Trans. Medical Imaging, 2019)

Weakly Supervised Deep Learning for Aortic Valve Finite Element Mesh Generation from 3D CT Images. - Daniel H. Pak; Minliang Liu; Shawn S. Ahn; Andrés Caballero; John A. Onofrey; Liang Liang; Wei Sun; James S. Duncan (IPMI, 2021)

TVnet: Automated Time-Resolved Tracking of the Tricuspid Valve Plane in MRI Long-Axis Cine Images with a Dual-Stage Deep Learning Pipeline. - Ricardo A. Gonzales; Jérôme Lamy; Felicia Seemann; Einar Heiberg; John A. Onofrey; Dana C. Peters (MICCAI (6), 2021)

Dual-Branch Squeeze-Fusion-Excitation Module for Cross-Modality Registration of Cardiac SPECT and CT. - Xiongchao Chen; Bo Zhou 009; Huidong Xie; Xueqi Guo; Jiazhen Zhang; Albert J. Sinusas; John A. Onofrey; Chi Liu 001 (MICCAI (6), 2022)

Multi-scale Super-Resolution Magnetic Resonance Spectroscopic Imaging with Adjustable Sharpness. - Siyuan Dong; Gilbert Hangel; Wolfgang Bogner; Georg Widhalm; Karl Rössler; Siegfried Trattnig; Chenyu You; Robin A. de Graaf; John A. Onofrey; James S. Duncan (MICCAI (6), 2022)

Flow-Based Visual Quality Enhancer for Super-Resolution Magnetic Resonance Spectroscopic Imaging. - Siyuan Dong; Gilbert Hangel; Eric Z. Chen; Shanhui Sun; Wolfgang Bogner; Georg Widhalm; Chenyu You; John A. Onofrey; Robin A. de Graaf; James S. Duncan (DGM4MICCAI@MICCAI, 2022)

Incremental Learning Meets Transfer Learning: Application to Multi-site Prostate MRI Segmentation. - Chenyu You; Jinlin Xiang; Kun Su; Xiaoran Zhang; Siyuan Dong; John A. Onofrey; Lawrence H. Staib; James S. Duncan (DeCaF/FAIR@MICCAI, 2022)

Supervised Deep Learning for Head Motion Correction in PET. - Tianyi Zeng; Jiazhen Zhang; Enette Mae Revilla; Eléonore V. Lieffrig; Xi Fang; Yihuan Lu; John A. Onofrey (MICCAI (4), 2022)

Atlas-Based Semantic Segmentation of Prostate Zones. - Jiazhen Zhang; Rajesh Venkataraman; Lawrence H. Staib; John A. Onofrey (MICCAI (5), 2022)

Adaptive data-driven motion detection and optimized correction for brain PET. - Enette Mae Revilla; Jean-Dominique Gallezot; Mika Naganawa; Takuya Toyonaga; Kathryn Fontaine; Tim Mulnix; John A. Onofrey; Richard E. Carson; Yihuan Lu (NeuroImage, 2022)

An objective evaluation method for head motion estimation in PET - Motion corrected centroid-of-distribution. - Chen Sun; Enette Mae Revilla; Jiazhen Zhang; Kathryn Fontaine; Takuya Toyonaga; Jean-Dominique Gallezot; Tim Mulnix; John A. Onofrey; Richard E. Carson; Yihuan Lu (NeuroImage, 2022)

Unsupervised Domain Adaptation by Cross-Prototype Contrastive Learning for Medical Image Segmentation. - Zhuotong Cai; Jingmin Xin; Siyuan Dong; Chenyu You; Peiwen Shi; Tianyi Zeng; Jiazhen Zhang; John A. Onofrey; Nanning Zheng 001; James S. Duncan (BIBM, 2023)

Multi-Task Deep Learning and Uncertainty Estimation for Pet Head Motion Correction. - Eléonore V. Lieffrig; Tianyi Zeng; Jiazhen Zhang; Kathryn Fontaine; Xi Fang; Enette Mae Revilla; Yihuan Lu; John A. Onofrey (ISBI, 2023)

Integrating Prostate Specific Antigen Density Biomarker Into Deep Learning Prostate MRI Lesion Segmentation Models. - Jiayang Zhong; Lawrence H. Staib; Rajesh Venkataraman; John A. Onofrey (ISBI, 2023)

Cross-Attention for Improved Motion Correction in Brain PET. - Zhuotong Cai; Tianyi Zeng; Eléonore V. Lieffrig; Jiazhen Zhang; Fuyao Chen; Takuya Toyonaga; Chenyu You; Jingmin Xin; Nanning Zheng 001; Yihuan Lu; James S. Duncan; John A. Onofrey (MLCN@MICCAI, 2023)

Fast Reconstruction for Deep Learning PET Head Motion Correction. - Tianyi Zeng; Jiazhen Zhang; Eléonore V. Lieffrig; Zhuotong Cai; Fuyao Chen; Chenyu You; Mika Naganawa; Yihuan Lu; John A. Onofrey (MICCAI (10), 2023)

Co-attention spatial transformer network for unsupervised motion tracking and cardiac strain analysis in 3D echocardiography. - Shawn S. Ahn; Kevinminh Ta; Stephanie Thorn; John A. Onofrey; Inga H. Melvinsdottir; Supum Lee; Jonathan Langdon; Albert J. Sinusas; James S. Duncan (Medical Image Anal., 2023)

DuSFE: Dual-Channel Squeeze-Fusion-Excitation co-attention for cross-modality registration of cardiac SPECT and CT. - Xiongchao Chen; Bo Zhou 009; Huidong Xie; Xueqi Guo; Jiazhen Zhang; James S. Duncan; Edward J. Miller; Albert J. Sinusas; John A. Onofrey; Chi Liu 001 (Medical Image Anal., 2023)

Symmetric Consistency with Cross-Domain Mixup for Cross-Modality Cardiac Segmentation. - Zhuotong Cai; Jingmin Xin; Siyuan Dong; John A. Onofrey; Nanning Zheng 001; James S. Duncan (ICASSP, 2024)

Monte-Carlo Frequency Dropout for Predictive Uncertainty Estimation in Deep Learning. - Tal Ze'evi; Rajesh Venkataraman; Lawrence H. Staib; John A. Onofrey (ISBI, 2024)

Patient-Specific Heart Geometry Modeling for Solid Biomechanics Using Deep Learning. - Daniel H. Pak; Minliang Liu; Theodore Kim; Liang Liang; Andrés Caballero; John A. Onofrey; Shawn S. Ahn; Yilin Xu; Raymond McKay; Wei Sun; Rudolph L. Gleason; James S. Duncan (IEEE Trans. Medical Imaging, 2024)

Reliable Prostate Cancer Risk Mapping From MRI Using Targeted and Systematic Core Needle Biopsy Histopathology. - Tal Ze'evi; Michael S. Leapman; Preston C. Sprenkle; Rajesh Venkataraman; Lawrence H. Staib; John A. Onofrey (IEEE Trans. Biomed. Eng., 2024)

Rate-In: Information-Driven Adaptive Dropout Rates for Improved Inference-Time Uncertainty Estimation. - Tal Zeevi; Ravid Shwartz-Ziv; Yann LeCun; Lawrence H. Staib; John A. Onofrey (CVPR, 2025)

Multi-view and Multi-scale Alignment for Contrastive Language-Image Pre-training in Mammography. - Yuexi Du; John A. Onofrey; Nicha C. Dvornek (IPMI (2), 2025)

SRE-CONV: Symmetric Rotation Equivariant Convolution for Biomedical Image Classification. - Yuexi Du; Jiazhen Zhang; Tal Zeevi; Nicha C. Dvornek; John A. Onofrey (ISBI, 2025)

Enhancing Uncertainty Estimation in Semantic Segmentation via Monte-Carlo Frequency Dropout. - Tal Zeevi; Lawrence H. Staib; John A. Onofrey (ISBI, 2025)

Improved Vessel Segmentation with Symmetric Rotation-Equivariant U-Net. - Jiazhen Zhang; Yuexi Du; Nicha C. Dvornek; John A. Onofrey (ISBI, 2025)

Conditional Convolution of Clinical Data Embeddings for Multimodal Prostate Cancer Classification. - Jiayang Zhong; Fuyao Chen; Lihui Chen; Dennis Shung; John A. Onofrey (ISBI, 2025)

A Flow-based Truncated Denoising Diffusion Model for super-resolution Magnetic Resonance Spectroscopic Imaging. - Siyuan Dong; Zhuotong Cai; Gilbert Hangel; Wolfgang Bogner; Georg Widhalm; Yaqing Huang; Qinghao Liang; Chenyu You; Chathura Kumaragamage; Robert K. Fulbright; Amit Mahajan; Amin Karbasi; et al. (Medical Image Anal., 2025)

Head Motion Degrades Machine Learning Classification of Alzheimer's Disease from Positron Emission Tomography. - Eléonore V. Lieffrig; Takuya Toyonaga; Jiazhen Zhang; John A. Onofrey (CoRR, 2025)

CT-Less Whole-Body Bone Segmentation of PET Images Using a Multimodal Deep Learning Network. - Nan Bao; Jiaxin Zhang; Zhikun Li; Shiyu Wei; Jiazhen Zhang; Stephen E. Greenwald; John A. Onofrey; Yihuan Lu; Lisheng Xu (IEEE J. Biomed. Health Informatics, 2025)

GMR-Conv: An Efficient Rotation and Reflection Equivariant Convolution Kernel Using Gaussian Mixture Rings. - Yuexi Du; Jiazhen Zhang; Nicha C. Dvornek; John A. Onofrey (CoRR, 2025)

Equivariant Imaging Biomarkers for Robust Unsupervised Segmentation of Histopathology. - Fuyao Chen; Yuexi Du; Tal Zeevi; Nicha C. Dvornek; John A. Onofrey (CoRR, 2025)

Spatially-Aware Evaluation of Segmentation Uncertainty. - Tal Zeevi; Eléonore V. Lieffrig; Lawrence H. Staib; John A. Onofrey (CoRR, 2025)