John A. Onofrey - Publications, H-index & Citations

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John A. Onofrey

yale university

20H-index

134Paper Count

1.6KCitation Count

Published Papers 23

Publication Date

PET Head Motion Estimation Using Supervised Deep Learning With Attention

IEEE Transactions on Medical Imaging

IF9.8

2025-10-13

PREAI

Zhuotong Cai; Tianyi Zeng; Jiazhen Zhang; Eléonore V. Lieffrig; Kathryn Fontaine; Chenyu You; Enette Mae Revilla; James S. Duncan; Jingmin Xin; Yihuan Lu; John A. Onofrey

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Comparative Performance of Machine Learning Models in Reducing Unnecessary Targeted Prostate Biopsies

European Urology Oncology

IF9.3

2025-02-08

PREAI

Fuyao Chen; Roxana Esmaili; Ghazal Khajir; Tal Zeevi; Moritz Gross; Michael Leapman; Preston Sprenkle; Amy C. Justice; Sandeep Arora; Jeffrey C. Weinreb; Michael Spektor; Steffan Huber; Peter A. Humphrey; Angelique Levi; Lawrence H. Staib; Rajesh Venkataraman; Darryl T. Martin; John A. Onofrey

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A Flow-based Truncated Denoising Diffusion Model for super-resolution Magnetic Resonance Spectroscopic Imaging

MEDICAL IMAGE ANALYSIS

IF11.8

2025-01-01

OAAI

Dong, Siyuan; Cai, Zhuotong; Hangel, Gilbert; Bogner, Wolfgang; Widhalm, Georg; Huang, Yaqing; Liang, Qinghao; You, Chenyu; Kumaragamage, Chathura; Fulbright, Robert K.; Mahajan, Amit; Karbasi, Amin; Onofrey, John A.; de Graaf, Robin A.; Duncan, James S.

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Aging-dependent loss of functional connectivity in a mouse model of Alzheimer's disease and reversal by mGluR5 modulator

MOLECULAR PSYCHIATRY

IF10.1

2024-10-18

OAAI

Mandino, Francesca; Shen, Xilin; Desrosiers-Gregoire, Gabriel; O'Connor, David; Mukherjee, Bandhan; Owens, Ashley; Qu, An; Onofrey, John; Papademetris, Xenophon; Chakravarty, M. Mallar; Strittmatter, Stephen M.; Lake, Evelyn M. R.

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Patient-Specific Heart Geometry Modeling for Solid Biomechanics Using Deep Learning

IEEE TRANSACTIONS ON MEDICAL IMAGING

IF9.8

2024-01-01

OAAI

Pak, Daniel H.; Liu, Minliang; Kim, Theodore; Liang, Liang; Caballero, Andres; Onofrey, John; Ahn, Shawn S.; Xu, Yilin; McKay, Raymond; Sun, Wei; Gleason, Rudolph; Duncan, James S.

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DuSFE: Dual-Channel Squeeze-Fusion-Excitation co-attention for cross-modality registration of cardiac SPECT and CT

MEDICAL IMAGE ANALYSIS

IF11.8

2023-08-01

OAAI

Chen, Xiongchao; Zhou, Bo; Xie, Huidong; Guo, Xueqi; Zhang, Jiazhen; Duncan, James S.; Miller, Edward J.; Sinusas, Albert J.; Onofrey, John A.; Liu, Chi

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Predicting tumor recurrence on baseline MR imaging in patients with early-stage hepatocellular carcinoma using deep machine learning

SCIENTIFIC REPORTS

IF3.9

2023-05-10

OAAI

Kucukkaya, Ahmet Said; Zeevi, Tal; Chai, Nathan Xianming; Raju, Rajiv; Haider, Stefan Philipp; Elbanan, Mohamed; Petukhova-Greenstein, Alexandra; Lin, MingDe; Onofrey, John; Nowak, Michal; Cooper, Kirsten; Thomas, Elizabeth; Santana, Jessica; Gebauer, Bernhard; Mulligan, David; Staib, Lawrence; Batra, Ramesh; Chapiro, Julius

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Co-attention spatial transformer network for unsupervised motion tracking and cardiac strain analysis in 3D echocardiography

MEDICAL IMAGE ANALYSIS

IF11.8

2023-02-01

OAAI

Ahn, Shawn S.; Ta, Kevinminh; Thorn, Stephanie L.; Onofrey, John A.; Melvinsdottir, Inga H.; Lee, Supum; Langdon, Jonathan; Sinusas, Albert J.; Duncan, James S.

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Deep learning-based attenuation map generation with simultaneously reconstructed PET activity and attenuation and low-dose application

PHYSICS IN MEDICINE AND BIOLOGY

IF3.4

2023-01-24

PREAI

Shi, Luyao; Zhang, Jiazhen; Toyonaga, Takuya; Shao, Dan; Onofrey, John A.; Lu, Yihuan

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Prediction of Adverse Pathology at Radical Prostatectomy in Grade Group 2 and 3 Prostate Biopsies Using Machine Learning

JCO CLINICAL CANCER INFORMATICS

IF2.8

2022-09-01

PREAI

Paulson, Nathan; Zeevi, Tal; Papademetris, Maria; Leapman, Michael S.; Onofrey, John A.; Sprenkle, Preston C.; Humphrey, Peter A.; Staib, Lawrence H.; Levi, Angelique W.

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Deep learning-based attenuation correction for whole-body PET - a multi-tracer study with 18F-FDG, 68 Ga-DOTATATE, and 18F-Fluciclovine

European Journal of Nuclear Medicine and Molecular Imaging

IF7.6

2022-03-12

OAAI

Toyonaga, Takuya; Shao, Dan; Shi, Luyao; Zhang, Jiazhen; Revilla, Enette Mae; Menard, David; Ankrah, Joseph; Hirata, Kenji; Chen, Ming-Kai; Onofrey, John A.; Lu, Yihuan

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Generation of synthetic PET images of synaptic density and amyloid from 18F-FDG images using deep learning

MEDICAL PHYSICS

IF3.2

2021-07-27

OAAI

Wang, Rui; Liu, Hui; Toyonaga, Takuya; Shi, Luyao; Wu, Jing; Onofrey, John Aaron; Tsai, Yu-Jung; Naganawa, Mika; Ma, Tianyu; Liu, Yaqiang; Chen, Ming-Kai; Mecca, Adam P.; O'Dell, Ryan S.; van Dyck, Christopher H.; Carson, Richard E.; Liu, Chi

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MVnet: automated time-resolved tracking of the mitral valve plane in CMR long-axis cine images with residual neural networks: a multi-center, multi-vendor study

JOURNAL OF CARDIOVASCULAR MAGNETIC RESONANCE

IF6.1

2021-03-01

OAAI

Gonzales, Ricardo A.; Seemann, Felicia; Lamy, Jerome; Mojibian, Hamid; Atar, Dan; Erlinge, David; Steding-Ehrenborg, Katarina; Arheden, Hakan; Hu, Chenxi; Onofrey, John A.; Peters, Dana C.; Heiberg, Einar

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Noise reduction with cross-tracer and cross-protocol deep transfer learning for low-dose PET

PHYSICS IN MEDICINE AND BIOLOGY

IF3.4

2020-09-14

PREAI

Liu, Hui; Wu, Jing; Lu, Wenzhuo; Onofrey, John A.; Liu, Yi-Hwa; Liu, Chi

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Sparse Data-Driven Learning for Effective and Efficient Biomedical Image Segmentation

ANNUAL REVIEW OF BIOMEDICAL ENGINEERING

IF0

2020-06-04

OAAI

Onofrey, John A.; Staib, Lawrence H.; Huang, Xiaojie; Zhang, Fan; Papademetris, Xenophon; Metaxas, Dimitris; Rueckert, Daniel; Duncan, James S.

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Deep learning-based attenuation map generation for myocardial perfusion SPECT

European Journal of Nuclear Medicine and Molecular Imaging

IF7.6

2020-03-26

PREAI

Shi, Luyao; Onofrey, John A.; Liu, Hui; Liu, Yi-Hwa; Liu, Chi

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An investigation of quantitative accuracy for deep learning based denoising in oncological PET

PHYSICS IN MEDICINE AND BIOLOGY

IF3.4

2019-08-21

110

PREAI

Lu, Wenzhuo; Onofrey, John A.; Lu, Yihuan; Shi, Luyao; Ma, Tianyu; Liu, Yaqiang; Liu, Chi

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Data-driven voluntary body motion detection and non-rigid event-by-event correction for static and dynamic PET

PHYSICS IN MEDICINE AND BIOLOGY

IF3.4

2019-03-08

PREAI

Lu, Yihuan; Gallezot, Jean-Dominique; Naganawa, Mika; Ren, Silin; Fontaine, Kathryn; Wu, Jing; Onofrey, John A.; Toyonaga, Takuya; Boutagy, Nabil; Mulnix, Tim; Panini, Vladimir Y.; Casey, Michael E.; Carson, Richard E.; Liu, Chi

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Segmenting the Brain Surface From CT Images With Artifacts Using Locally Oriented Appearance and Dictionary Learning

IEEE TRANSACTIONS ON MEDICAL IMAGING

IF9.8

2019-02-01

OAAI

Onofrey, John A.; Staib, Lawrence H.; Papademetris, Xenophon

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Respiratory Motion Compensation for PET/CT with Motion Information Derived from Matched Attenuation-Corrected Gated PET Data

JOURNAL OF NUCLEAR MEDICINE

IF9.1

2018-02-09

OAAI

Lu, Yihuan; Fontaine, Kathryn; Mulnix, Tim; Onofrey, John A.; Ren, Silin; Panin, Vladimir; Jones, Judson; Casey, Michael E.; Barnett, Robert; Kench, Peter; Fulton, Roger; Carson, Richard E.; Liu, Chi

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Research Directions