NCI/NSF Workshop on Operations Research Applied to Radiation Therapy Washington, DC, February 7-9, 2002. - Eva K. Lee; Joseph Deasy; Mark P. Langer; Ronald L. Rardin; Jim A. Deye; Frank J. Mahoney (Ann. Oper. Res., 2003)

microRT: A Conformal Small Animal Irradiator. - Daniel A. Low; Sasa Mutic; Perry Grigsby; Milos Vicic; Joseph Deasy; Andrew Hope (ISBI, 2004)

Compensation of breathing motion artifacts in thoracic PET images by wavelet-based deconvolution. - Issam El-Naqa; Daniel A. Low; Jeffrey D. Bradley; Milos Vicic; Joseph Deasy (ISBI, 2006)

A collaboratory for radiation therapy treatment planning optimization research. - Joseph Deasy; Eva K. Lee; T. Bortfeld; Mark P. Langer; K. Zakarian; J. Alaly; Y. Zhang; H. Liu; R. Mohan; R. Ahuja; A. Pollack; J. Purdy; et al. (Ann. Oper. Res., 2006)

Automated Estimation of the Biophysical Target for Radiotherapy Treatment Planning using Multimodality Image Analysis. - Issam El-Naqa; Deshan Yang; Joseph Deasy (ICIP (5), 2007)

Level set motion assisted non-rigid 3D image registration. - Deshan Yang; Joseph O. Deasy; Daniel A. Low; Issam El-Naqa (Image Processing, 2007)

Current role of PET in oncology: Potentials and challenges in the management of non-small cell lung cancer. - Phaneendra K. Yalavarthy; Daniel A. Low; Camille Noel; Zhouping Wei; Deshan Yang; Aditya P. Apte; Jeffrey D. Bradley; Joseph Deasy; Issam El-Naqa (ACSCC, 2008)

A fast inverse consistent deformable image registration method based on symmetric optical flow computation. - Deshan Yang; Hua Li; Daniel A. Low; Joseph O. Deasy; Issam El-Naqa (ACSCC, 2008)

Decision Fusion of Machine Learning Models to Predict Radiotherapy-Induced Lung Pneumonitis. - Shiva K. Das; Shifeng Chen; Joseph O. Deasy; Sumin Zhou; Fang-Fang Yin; Lawrence B. Marks (ICMLA, 2008)

Nonlinear Kernel-Based Approaches for Predicting Normal Tissue Toxicities. - Issam El-Naqa; Jeffrey D. Bradley; Joseph Deasy (ICMLA, 2008)

Surface Reconstruction From Non-parallel Curve Networks. - Lu Liu 012; Chandrajit Bajaj; Joseph Deasy; Daniel A. Low; Tao Ju 001 (Comput. Graph. Forum, 2008)

Improving Clinical Relevance in Ensemble Support Vector Machine Models of Radiation Pneumonitis Risk. - Todd W. Schiller; Yixin Chen 001; Issam El-Naqa; Joseph O. Deasy (ICMLA, 2009)

Exploring feature-based approaches in PET images for predicting cancer treatment outcomes. - Issam El-Naqa; Perry Grigsby; Aditya P. Apte; Elizabeth Kidd; Eric Donnelly; Divya Khullar; Summer Chaudhari; Deshan Yang; Martin Schmitt; Richard Laforest; Wade L. Thorstad; Joseph Deasy (Pattern Recognit., 2009)

Predicting Local Failure in Lung Cancer Using Bayesian Networks. - Jung Hun Oh; Jeffrey Craft; Rawan Al-Lozi; Manushka Vaidya; Yifan Meng; Joseph O. Deasy; Jeffrey D. Bradley; Issam El-Naqa (ICMLA, 2010)

Modeling radiation-induced lung injury risk with an ensemble of support vector machines. - Todd W. Schiller; Yixin Chen 001; Issam El-Naqa; Joseph O. Deasy (Neurocomputing, 2010)

Automatic Bone and Marrow Extraction from Dual Energy CT through SVM Margin-Based Multi-Material Decomposition Model Selection. - Harini Veeraraghavan; Duc Fehr; Charles Ross Schmidtlein; Sinchun Hwang; Joseph O. Deasy (MLMI, 2014)

Inference of radio-responsive gene regulatory networks using the graphical lasso algorithm. - Jung Hun Oh; Joseph O. Deasy (BMC Bioinform., 2014)

SITDEM: A simulation tool for disease/endpoint models of association studies based on single nucleotide polymorphism genotypes. - Jung Hun Oh; Joseph O. Deasy (Comput. Biol. Medicine, 2014)

Modeling the Relationship between Fluorodeoxyglucose Uptake and Tumor Radioresistance as a Function of the Tumor Microenvironment. - Jeho Jeong; Joseph O. Deasy (Comput. Math. Methods Medicine, 2014)

Automatic classification of prostate cancer Gleason scores from multiparametric magnetic resonance images. - Duc Fehr; Harini Veeraraghavan; Andreas Wibmer; Tatsuo Gondo; Kazuhiro Matsumoto; Herbert Alberto Vargas; Evis Sala; Hedvig Hricak; Joseph O. Deasy (Proc. Natl. Acad. Sci. USA, 2015)

Transcriptional responses to ultraviolet and ionizing radiation: An approach based on graph curvature. - Yongxin Chen; Jung Hun Oh; Romeil Sandhu; Sangkyu Lee; Joseph O. Deasy; Allen R. Tannenbaum (BIBM, 2016)

Automatic detection and tracking of longitudinal changes of multiple bone metastases from dual energy CT. - Duc Fehr; Charles Ross Schmidtlein; Sinchun Hwang; Joseph O. Deasy; Harini Veeraraghavan (ISBI, 2016)

A literature mining-based approach for identification of cellular pathways associated with chemoresistance in cancer. - Jung Hun Oh; Joseph O. Deasy (Briefings Bioinform., 2016)

Preconditioned Random Forest Regression: Application to Genome-Wide Study for Radiotherapy Toxicity Prediction. - Sangkyu Lee; Sarah Kerns; Barry Rosenstein; Harry Ostrer; Joseph O. Deasy; Jung Hun Oh (BCB, 2017)

Interpretable Spiculation Quantification for Lung Cancer Screening. - Wookjin Choi; Saad Nadeem; Sadegh Riyahi; Joseph O. Deasy; Allen R. Tannenbaum; Wei Lu 025 (ShapeMI@MICCAI, 2018)

Tumor-Aware, Adversarial Domain Adaptation from CT to MRI for Lung Cancer Segmentation. - Jue Jiang; Yu-Chi Hu; Neelam Tyagi; Pengpeng Zhang; Andreas Rimner; Gig S. Mageras; Joseph O. Deasy; Harini Veeraraghavan (MICCAI (2), 2018)

Quantification of Local Metabolic Tumor Volume Changes by Registering Blended PET-CT Images for Prediction of Pathologic Tumor Response. - Sadegh Riyahi; Wookjin Choi; Chia-Ju Liu; Saad Nadeem; Shan Tan; Hualiang Zhong; Wengen Chen; Abraham J. Wu; James G. Mechalakos; Joseph O. Deasy; Wei Lu 025 (DATRA/PIPPI@MICCAI, 2018)

Controlled and Uncontrolled Stochastic Norton-Simon-Massagué Tumor Growth Models. - Zehor Belkhatir; Michele Pavon; James C. Mathews; Maryam Pouryahya; Joseph O. Deasy; Larry Norton; Allen R. Tannenbaum (CDC, 2019)

Cardio-Pulmonary Substructure Segmentation of CT Images Using Convolutional Neural Networks. - Rabia Haq; Alexandra Hotca; Aditya P. Apte; Andreas Rimner; Joseph O. Deasy; Maria Thor (AIRT@MICCAI, 2019)

Integrating Cross-modality Hallucinated MRI with CT to Aid Mediastinal Lung Tumor Segmentation. - Jue Jiang; Jason Hu; Neelam Tyagi; Andreas Rimner; Sean L. Berry; Joseph O. Deasy; Harini Veeraraghavan (MICCAI (6), 2019)

Cross-modality (CT-MRI) prior augmented deep learning for robust lung tumor segmentation from small MR datasets. - Jue Jiang; Yu-Chi Hu; Neelam Tyagi; Pengpeng Zhang; Andreas Rimner; Joseph O. Deasy; Harini Veeraraghavan (CoRR, 2019)

Comparison of Patch-Based Conditional Generative Adversarial Neural Net Models with Emphasis on Model Robustness for Use in Head and Neck Cases for MR-Only planning. - Peter Klages; Ilyes Benslimane; Sadegh Riyahi; Jue Jiang; Margie Hunt; Joseph O. Deasy; Harini Veeraraghavan; Neelam Tyagi (CoRR, 2019)

Kernel Wasserstein Distance. - Jung Hun Oh; Maryam Pouryahya; Aditi Iyer; Aditya P. Apte; Allen R. Tannenbaum; Joseph O. Deasy (CoRR, 2019)

Multiple Resolution Residually Connected Feature Streams for Automatic Lung Tumor Segmentation From CT Images. - Jue Jiang; Yu-Chi Hu; Chia-Ju Liu; Darragh Halpenny; Matthew D. Hellmann; Joseph O. Deasy; Gig S. Mageras; Harini Veeraraghavan (IEEE Trans. Medical Imaging, 2019)

A Vectorial Approach to Unbalanced Optimal Mass Transport. - Jiening Zhu; Rena Elkin; Jung Hun Oh; Joseph O. Deasy; Allen R. Tannenbaum (IEEE Access, 2020)

A novel kernel Wasserstein distance on Gaussian measures: An application of identifying dental artifacts in head and neck computed tomography. - Jung Hun Oh; Maryam Pouryahya; Aditi Iyer; Aditya P. Apte; Joseph O. Deasy; Allen R. Tannenbaum (Comput. Biol. Medicine, 2020)

Multiple resolution residual network for automatic thoracic organs-at-risk segmentation from CT. - Hyemin Um; Jue Jiang; Maria Thor; Andreas Rimner; Leo Luo; Joseph O. Deasy; Harini Veeraraghavan (CoRR, 2020)

PSIGAN: Joint Probabilistic Segmentation and Image Distribution Matching for Unpaired Cross-Modality Adaptation-Based MRI Segmentation. - Jue Jiang; Yu-Chi Hu; Neelam Tyagi; Andreas Rimner; Nancy Lee; Joseph O. Deasy; Sean Berry; Harini Veeraraghavan (IEEE Trans. Medical Imaging, 2020)

PathCNN: interpretable convolutional neural networks for survival prediction and pathway analysis applied to glioblastoma. - Jung Hun Oh; Wookjin Choi; Euiseong Ko; Mingon Kang; Allen R. Tannenbaum; Joseph O. Deasy (Bioinform., 2021)

Reproducible and Interpretable Spiculation Quantification for Lung Cancer Screening. - Wookjin Choi; Saad Nadeem; Sadegh R. Alam; Joseph O. Deasy; Allen R. Tannenbaum; Wei Lu 025 (Comput. Methods Programs Biomed., 2021)

Deep cross-modality (MR-CT) educed distillation learning for cone beam CT lung tumor segmentation. - Jue Jiang; Sadegh Riyahi Alam; Ishita Chen; Perry Zhang; Andreas Rimner; Joseph O. Deasy; Harini Veeraraghavan (CoRR, 2021)

Nested-block self-attention for robust radiotherapy planning segmentation. - Harini Veeraraghavan; Jue Jiang; Elguindi Sharif; Sean L. Berry; Ifeanyirochukwu Onochie; Aditya P. Apte; Laura Cervino; Joseph O. Deasy (CoRR, 2021)

Unpaired cross-modality educed distillation (CMEDL) applied to CT lung tumor segmentation. - Jue Jiang; Andreas Rimner; Joseph O. Deasy; Harini Veeraraghavan (CoRR, 2021)

Stochastic Norton-Simon-Massagué Tumor Growth Modeling: Controlled and Mixed-Effect Uncontrolled Analysis. - Zehor Belkhatir; Michele Pavon; James C. Mathews; Maryam Pouryahya; Joseph O. Deasy; Larry Norton; Allen R. Tannenbaum (IEEE Trans. Control. Syst. Technol., 2021)

The maximum entropy principle for compositional data. - Corey Weistuch; Jiening Zhu; Joseph O. Deasy; Allen R. Tannenbaum (BMC Bioinform., 2022)

Automated and Clinically Optimal Treatment Planning for Cancer Radiotherapy. - Masoud Zarepisheh; Linda Hong; Ying Zhou; Qijie Huang; Jie Yang; Gourav Jhanwar; Hai D. Pham; Pinar Dursun; Pengpeng Zhang; Margie Hunt; Gig S. Mageras; Jonathan T. Yang; et al. (INFORMS J. Appl. Anal., 2022)

aWCluster: A Novel Integrative Network-Based Clustering of Multiomics for Subtype Analysis of Cancer Data. - Maryam Pouryahya; Jung Hun Oh; Pedram Javanmard; James C. Mathews; Zehor Belkhatir; Joseph O. Deasy; Allen R. Tannenbaum (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Unpaired Cross-Modality Educed Distillation (CMEDL) for Medical Image Segmentation. - Jue Jiang; Andreas Rimner; Joseph O. Deasy; Harini Veeraraghavan (IEEE Trans. Medical Imaging, 2022)

Optimal Transport for Kernel Gaussian Mixture Models. - Jung Hun Oh; Rena Elkin; Anish Kumar Simhal; Jiening Zhu; Joseph O. Deasy; Allen R. Tannenbaum (CoRR, 2023)

Geometric graph neural networks on multi-omics data to predict cancer survival outcomes. - Jiening Zhu; Jung Hun Oh; Anish K. Simhal; Rena Elkin; Larry Norton; Joseph O. Deasy; Allen R. Tannenbaum (Comput. Biol. Medicine, 2023)

ROE (Radiotherapy Outcomes Estimator): An open-source tool for optimizing radiotherapy prescriptions. - Aditi Iyer; Aditya P. Apte; Ethan Bendau; Maria Thor; Ishita Chen; Jacob Shin; Abraham J. Wu; Daniel Gomez; Andreas Rimner; Ellen Yorke; Joseph O. Deasy; Andrew Jackson (Comput. Methods Programs Biomed., 2023)

Tumor aware recurrent inter-patient deformable image registration of computed tomography scans with lung cancer. - Jue Jiang; Chloe Min Seo Choi; Maria Thor; Joseph O. Deasy; Harini Veeraraghavan (CoRR, 2024)

Multi-omic integrated curvature study on pan-cancer genomic data. - Jiening Zhu; Anh Phong Tran; Joseph O. Deasy; Allen R. Tannenbaum (Math. Control. Signals Syst., 2024)

Wasserstein HOG: Local Directionality Extraction via Optimal Transport. - Jiening Zhu; Harini Veeraraghavan; Jue Jiang; Jung Hun Oh; Larry Norton; Joseph O. Deasy; Allen R. Tannenbaum (IEEE Trans. Medical Imaging, 2024)

Large language model trained on clinical oncology data predicts cancer progression. - Menglei Zhu; Hui Lin; Jue Jiang; Abbas J. Jinia; Justin Jee; Karl Pichotta; Michele Waters; Doori Rose; Nikolaus Schultz; Sulov Chalise; Lohit Valleru; Olivier Morin; et al. (npj Digit. Medicine, 2025)