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MIPG Publications, Patents & Recognitions

 

MIPG Publications: 7/1/2024 – 6/30/2025

  1. Hao Y, Udupa JK, Tong Y, Wu C, McDonough JM, Gogel S, Mayer OH, Alnoury M, Cahill PJ, Anari JB. Quantifying normal diaphragmatic motion and shape and their developmental changes via dynamic MRI. CHEST Pulmonary. 2025 March;3(1):100115.
  2. Liu T, Bai Q, Torigian DA, Tong Y, Udupa JK. VSmTrans: A hybrid paradigm integrating self-attention and convolution for 3D medical image segmentation. Med Image Anal. 2024 Dec;98:103295. doi: 10.1016/j.media.2024.103295. Epub 2024 Aug 24. PMID: 39217673; PMCID: PMC11381179.
  3. Tong Y, Udupa JK, McDonough JM, Wu C, Xie L, Rajapakse CS, Gogel S, Sarkar S, Mayer OH, Anari JB, Torigian DA, Cahill PJ. Characterizing Lung Parenchymal Aeration via Standardized Signal Intensity from Free-breathing 4D Dynamic MRI in Phantoms, Healthy Children, and Pediatric Patients with Thoracic Insufficiency Syndrome. Radiol Cardiothorac Imaging. 2024 Aug;6(4):e230262. doi: 10.1148/ryct.230262. PMID: 39051878; PMCID: PMC11369656.
  4. Xie L, Xu Y, Zheng M, Chen Y, Sun M, Archer MA, Mao W, Tong Y, Wan Y. An anthropomorphic diagnosis system of pulmonary nodules using weak annotation-based deep learning. Comput Med Imaging Graph. 2024 Dec;118:102438. doi: 10.1016/j.compmedimag.2024.102438. Epub 2024 Oct 10. PMID: 39426342; PMCID: PMC11620937.
  5. McCarthy BE, Feng R, Torigian DA, Tong Y, Fritz JS, Minhas JK, Mazurek JA, Smith KA, Palevsky HI, Pugliese SC, Homer NZ, MacLean MR, Udupa JK, Al-Naamani N. Epicardial Adipose Tissue as an Independent Risk Factor for Mortality in Pulmonary Arterial Hypertension. Chest. 2025 May;167(5):1481-1492. doi: 10.1016/j.chest.2024.11.020. Epub 2024 Nov 28. PMID: 39613149; PMCID: PMC12106954.
  6. Lomer NB, Ashoobi MA, Ahmadzadeh AM, Sotoudeh H, Tabari A, Torigian DA. MRI-based Radiomics for Predicting Prostate Cancer Grade Groups: A Systematic Review and Meta-analysis of Diagnostic Test Accuracy Studies. Acad Radiol. 2025 Jun;32(6):3429-3452. doi: 10.1016/j.acra.2024.12.006. Epub 2024 Dec 31. PMID: 39743477.
  7. Long M, Alnoury M, Udupa JK, Tong Y, Wu C, Poole N, Mannikeri S, Ky B, Feigenberg SJ, Zou JW, O'Reilly S, Torigian DA. Prediction of Radiation Therapy Induced Cardiovascular Toxicity from Pretreatment CT Images in Patients with Thoracic Malignancy via an Optimal Biomarker Approach. Acad Radiol. 2025 Apr;32(4):1895-1905. doi: 10.1016/j.acra.2025.01.012. Epub 2025 Jan 26. PMID: 39870564; PMCID: PMC11981848.
  8. Ewing JN, Gala Z, Voytik M, Broach RB, Udupa JK, Torigian DA, Tong Y, Fischer JP. A cross-sectional survey investigating surgeon perceptions of pre-operative risk prediction models incorporating radiomic features. Hernia. 2025 Feb 18;29(1):97. doi: 10.1007/s10029-025-03292-0. PMID: 39966191.
  9. Ahmadzadeh AM, Lomer NB, Torigian DA. Radiomics and machine learning models for diagnosing microvascular invasion in cholangiocarcinoma: a systematic review and meta-analysis of diagnostic test accuracy studies. Clin Imaging. 2025 May;121:110456. doi: 10.1016/j.clinimag.2025.110456. Epub 2025 Mar 13. PMID: 40088548.
  10. Pierson SK, Brandstadter JD, Torigian DA, Bagg A, Lechowicz MJ, Alapat D, Casper C, Chadburn A, Chandrakasan S, Dispenzieri A, Fosså A, Hoffmann C, Ide M, Kurzrock R, Mukherjee S, Nasta S, Navarro JT, Noy A, Oksenhendler E, Bustamante MS, Shyamsundar S, Streetly M, Wong RSM, Zhang L, Lim MS, Srkalovic G, van Rhee F, Fajgenbaum DC. Characterizing the heterogeneity of Castleman disease and oligocentric subtype: findings from the ACCELERATE registry. Blood Adv. 2025 Apr 22;9(8):1952-1965. doi: 10.1182/bloodadvances.2024014391. PMID: 39951615; PMCID: PMC12018988.
  11. Fanta O, Patil S, Werner T, Torigian DA, Alavi A. Reproducibility of 18F-Sodium Fluoride Positron Emission Tomography for Assessing Microcalcification in Coronary Arterial and Thoracic Aortic Atherosclerosis: Is the Signal below the Resolution of PET? Curr Cardiol Rep. 2025 May 14;27(1):88. doi: 10.1007/s11886-025-02240-9. PMID: 40369378; PMCID: PMC12078425.
  12. Hassani S, Tong Y, Lomer NB, Udupa JK, Wu C, McDonough JM, Gogel S, Mayer OH, Biko DM, Cahill PJ, Anari JB, Torigian DA. Comparative analysis of thoracic structure and function using CT and dynamic MRI in pediatric thoracic insufficiency syndrome with and without neuromuscular disease. Spine Deform. 2025 May 6. doi: 10.1007/s43390-025-01095-y. Epub ahead of print. PMID: 40327258.
  13. Tong Y, Udupa JK, McDonough JM, Xie L, Wu C, Akhtar Y, Hosseini M, Alnoury M, Shaghaghi S, Gogel S, Biko DM, Mayer OH, Torigian DA, Cahill PJ, Anari JB. Do Rib-Based Anchors Impair Chest Wall Motion in Early Onset Scoliosis? - A Novel Investigation via Dynamic MRI. J Pediatr Orthop. 2025 Jun 4. doi: 10.1097/BPO.0000000000003015. Epub ahead of print. PMID: 40488411.
  14. Liu T, Li J, Torigian DA, Tong Y, Xiong Q, Zhang K, Udupa JK. Diffusion semantic segmentation model: A generative model for medical image segmentation based on joint distribution. Med Phys. 2025 Jul;52(7):e17928. doi: 10.1002/mp.17928. Epub 2025 Jun 8. PMID: 40483601.
  15. Lomer NB, Abdi S, Ashoobi MA, Ahmadzadeh AM, Ghasemi A, Torigian DA. Accuracy of CT-Based Radiomics Models for Preoperative Grading of Clear Cell Renal Cell Carcinoma: A Systematic Review and Meta-analysis. Acad Radiol. 2025 Jun 16:S1076-6332(25)00526-4. doi: 10.1016/j.acra.2025.05.049. Epub ahead of print. PMID: 40527677.
  16. Mortazi A, Udupa JK, Hosseini M, Tong Y, Torigian DA. Virtual cutaneous area severity index (vCASI): A comprehensive methodology for quantitative skin disease assessment on positron emission tomography images. Eur J Nucl Med Mol Imaging. 2025 Jun 23. doi: 10.1007/s00259-025-07423-8. Epub ahead of print. PMID: 40545498

Conference Papers (Peer Reviewed Full Papers): 7/1/2024 – 6/30/2025

  1. Alnoury M, Udupa JK, Tong Y, Liu T, Akhtar Y, Torigian DA.: Body composition analysis: single slice vs. volumetric measures. Proc SPIE 13411, Medical Imaging 2025: Imaging Informatics, 134110X (10 April 2025); https://doi.org/10.1117/12.3047376
  2. Hao Y, Udupa JK, Tong Y, Wu C, Gogel S, Biko DM, Mayer OH, McDonough JM, Cahill PJ, Torigian DA, Anari JB.: Respiratory volume prediction for pediatric TIS patients with MAGEC rod treatment from pre-operative dynamic MRI and chest radiographs. Proc SPIE 13405, Medical Imaging 2025: Physics of Medical Imaging, 134051T (8 April 2025); https://doi.org/10.1117/12.3047707
  3. Ling Z, Udupa JK, Tong L, McDonough JM, Gogel S, Mayer O, Biko D, Cahill PJ, Anari JB, Tong Y, Torigian DA.: Normalizing thoracic morphometric measures for size differences among pediatric patients and normal subjects. Proc SPIE 13411, Medical Imaging 2025: Imaging Informatics, 1341119 (10 April 2025); https://doi.org/10.1117/12.3047138
  4. Tong Y, Xie L, Odhner D, Liu T, Torigian DA, Udupa JK.: Hybrid foundation models: an investigation of foundation anatomy model and foundation segmentation model (FAM-FSM) on thoracic CT images for radiation therapy planning. Proc SPIE 13408, Medical Imaging 2025: Image-Guided Procedures, Robotic Interventions, and Modeling, 134082K (7 April 2025); https://doi.org/10.1117/12.3047793
  5. Xie L, Tong Y, Torigian DA, Wu C, Gogel S, Biko DM, Mayer OH, McDonough JM, Cahill PJ, Anari JB, Udupa JK.: Semi-automatic anatomy segmentation in thoracic dynamic MRI based on Segment Anything Model. Proc SPIE 13406, Medical Imaging 2025: Image Processing, 1340635 (11 April 2025); https://doi.org/10.1117/12.3047893
  6. Li J, Udupa JK, Torigian DA, Tong Y, Xiong Q, Zhang K, Liu T.: Diffusion semantic segmentation: a generative segmentation model based on joint distributions. Proc SPIE 13406, Medical Imaging 2025: Image Processing, 1340620 (11 April 2025); https://doi.org/10.1117/12.3047126
  7. Tong Y, Udupa JK, McDonough JM, Wu C, Xie L, Hao Y, Gogel S, Mayer OH, Biko DM, Torigian DA, Cahill PJ, Anari JB.: Dynamic MRI-guided surgery planning and treatment evaluation for pediatric patients with TIS: database, methodology, results, and analysis. Proc SPIE 13408, Medical Imaging 2025: Image-Guided Procedures, Robotic Interventions, and Modeling, 134082T (7 April 2025); https://doi.org/10.1117/12.3047149
  8. Shaghaghi S, Udupa JK, Tong Y, Akhtar Y, Hosseini M, Al-Noury M, Wu C, Xie L, Hao Y, Hassani S, Gogel S, Biko DM, Mayer OH, McDonough JM, Cahill PJ, Anari JB, Torigian DA.: Association between respiratory volumes estimated from free-breathing dynamic MRI and sagittal spinal curvature in pediatric patients with thoracic insufficiency syndrome. Proc SPIE 13408, Medical Imaging 2025: Image-Guided Procedures, Robotic Interventions, and Modeling, 134082Q (7 April 2025); https://doi.org/10.1117/12.3047058
  9. Dai J, Udupa JK, Torigian DA, Tong Y, Liu T.: A one-shot/few-shot interactive segmentation method for CT image segmentation. Proc SPIE 13407, Medical Imaging 2025: Computer-Aided Diagnosis, 134073D (4 April 2025); https://doi.org/10.1117/12.3047122
    Nln Y, Akhtar Y, Tong Y, Liu T, Wu C, Kim D, Costin M, Fabula O, Cao S, Zhang K, Xu Z, Torigian DA, Udupa JK.: Anatomically ROI and IOI informed hybrid U-Net model for abdominal object segmentation in CT images. Proc SPIE 13410, Medical Imaging 2025: Clinical and Biomedical Imaging, 1341016 (2 April 2025); https://doi.org/10.1117/12.3047274
  10. Li J, Udupa JK, Tong Y, Torigian DA.: Prediction of disease quantification via PET/CT images and auto-segmentation of target objects. Proc SPIE 13410, Medical Imaging 2025: Clinical and Biomedical Imaging, 134101Q (2 April 2025); https://doi.org/10.1117/12.3047268
  11. Wang B, Pan H, Aboah A, Zhang Z, Keles E, Torigian D, Turkbey B, Krupinski E, Udupa J, Bagci U. GazeGNN: A gaze-guided graph neural network for chest x-ray classification. Proc 2024 IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), pp. 2183-2192. doi: 10.1109/WACV57701.2024.00219.
 

Patents

  1. Udupa JK, Samarasekera S. Extraction of fuzzy object information in multidimensional images for quantifying MS lesions of the brain. US patent US-5,812,691, September 1998.
  2. Nyul LG, Udupa JK. A method of standardizing the MR image intensity scale. US patent US-6,284,216, June 2003.
  3. Saha PK, Udupa JK. Scale-based image filtering of magnetic resonance data. US patent US-6,885,762 B2, April 2005.
  4. Udupa JK, Liu J. Segmentation method using an oriented active shape model. US letters, patent: US-8,050,473, November 2011.
  5. Udupa JK, Souza A, Grevera GJ, Odhner D. Image slice segmentation using midpoints of contour anchor points. US patent US-8,270,696 B2, September 18, 2012. 
  6. Udupa JK, Odhner D, Tong Y, Torigian DA. Interactive non-uniformity correction and intensity standardization of MR images. US patent US 10,043,250 B2, August 7, 2018. 
  7. Udupa JK, Liu T, Tong Y, Odhner D, Torigian DA. Quantification and staging of  body-wide tissue composition and of abnormal states on medical images via Automatic Anatomy Recognition. US patent 11,443,433 B2, September 13, 2022.
  8. Udupa JK, Agrawal V, Tong Y, Torigian DA. Deep learning architecture for analyzing medical images for body region recognition and delineation. US patent 11,995,830 B2, May 28, 2024. 
  9. Udupa JK, Tong Y, Torigian DA, Hao Y, Sun C, McDonough JM, Cahill PJ. Quantitative dynamic MRI (QDMRI) analysis and virtual growing child (VGC) systems and methods for treating respiratory anomalies. US patent 12,336,839, 2025.
  10. Udupa JK, Odhner D, Tong Y, Torigian DA. Applications of automatic anatomy recognition in medical tomographic imagery based on fuzzy anatomy models. US patent US 12,223,655 B2, February 11, 2025. 
     

Recognitions

  1. Recognition in the AI community: We published a method and an AI model called VSmTrans for segmenting objects body wide in tomographic images during the previous reporting period: Liu T, Bai Q, Drew A. Torigian DA, Tong Y, Udupa JK. VSmTrans: A Hybrid Paradigm  Integrating Self-attention and Convolution for 3D Medical Image Segmentation, Medical Image Analysis, 98, 103295, 2024. The publicly shared model for VSmTrans overwhelmingly topped the rank list in a recent large-scale independent external benchmarking, which compared 20 different competitive methods (Bassi PRAS, Zhou Z, et al. Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation? 2024/11/06. doi: 10.48550/arXiv.2411.03670) using ~9K training CT scans, and ~5K test scans. VSmTrans achieved an overall Dice accuracy of 89.8% on 25 objects, while the closest 2nd rank method could segment only 9 objects yielding a Dice accuracy of 87.4%. 
  2. Tong Y, Udupa JK, McDonough JM, Wu C, Qiu C, Lott, C, Galagedera N, Anari JB, Torigian DA, Patrick J. Cahill PJ. A Novel Imaging Study to Quantify Respiratory Function in Early Onset Scoliosis-Introducing Quantitative Dynamic Magnetic Resonance Imaging (QdMRI). Russel A Hibbs best science paper award in Scoliosis Research Society (SRS) 55th Annual Meeting, online, Sep. 9 - Sep. 13, 2020.
  3. Tong Y, Udupa JK, McDonough JM, Wu C, Qiu C, Lott, C, Galagedera N, Anari JB, Torigian DA, Patrick J. Cahill PJ. 3. Rib-based Anchors do not Impair Chest Wall Motion in Early Onset Scoliosis. Best science paper award in 14th International Congress on Early Onset Scoliosis (2020 ICEOS Virtual Meeting), November 14, 2020.
  4.  What’s New in Pediatric Orthopaedics 2024. An editorial published in Journal of Bone and Joint Surgery, February 19, 2024, under Ortho Buzz for Surgeons by Hardesty CK. Our QdMRI work(Tong et al. JBJS, 2023;105(1):53-62) was cited as one of the 5 most compelling studies published in general and subspecialty journals between October 2022 and September 2023. Available from: https://orthobuzz.jbjs.org/2024/02/19/whats-new-in-pediatric-orthopaedics-2024/
  5. Hosseini M, Udupa JK, Hao Y, Tong Y, Akhtar Y, Shaghaghi S, Al-Noury M, Wu C, McDonough JM, Cahill PJ, Anari JB, Torigian DA. Assessment of 3D hemi-diaphragmatic motion via free-breathing dynamic MRI in pediatric thoracic insufficiency syndrome. Annual Conference and Exhibition of the Radiological Society of North America, 2023, Trainee Research Prize.
  6. Udupa JK, Liu T, Jin C, Zhao L, Odhner D, Tong Y, Agrawal V, Pednekar GV, Nag S, Kotia T, Goodman M, Wileyto EP, Mihailidis D, Lukens JN, Berman AT, Stambaugh J, Lim T, Chowdary R, Jalluri D, Jabbour SK, Kim S, Reyhan M, Robinson C, Thorstad W, Choi JI, Press R, Simone CB 2nd , Camaratta J, Owens S, Torigian DA. Combining natural and artificial intelligence for robust automatic anatomy segmentation: Application in neck and thorax auto-contouring for radiation therapy planning, Medical Physics, 49: 7118-7149, 2022. This paper figured in the front cover of that issue of the journal, and it was the most downloaded for that journal during that year.
  7. Drew Torigian, MD, 2024 Top Scholar by ScholarGPS (top percentage rank 0.41% over all fields out of ~29M ranked scholars, and top percentage rank 0.52% in radiology out of ~200k ranked scholars).
  8. Drew Torigian, MD, Best in Pennsylvania Magazine, Doctors 2024, for excellence in radiology.

Resources

  1. CAVASS Software
  2. VGC Database (QdMRI)
    -Tong Y, Udupa JK, Torigian DA, Cahill PJ. A normative database of free-breathing pediatric thoracic 4D dynamic MRI images [Dataset]. Dryad; 2024 - [cited 2024 May 15]. Available from: doi: 10.5061/dryad.vmcvdnczf (this data is available via NIH / NHLBI BioData Catalyst (BDC) July (2025) release).
  3. Other Databases (CT, PET/CT) 

Recent Major Publications Before 7/1/2024

  1. Shahait M, Usamentiaga R, Tong Y, Sandberg A, Lee DI, Udupa JK, Torigian DA. MRI-based radiomic features of the urinary bladder wall identify patients with moderate-to-severe international prostate symptom score. World J Urol. 2024 Jun 13;42(1):375. doi: 10.1007/s00345-024-05081-3. PMID: 38872048; PMCID: PMC11176201. 
  2. Donuru A, Torigian DA, Nachiappan AC. Grayscale Inversion to aid Diagnosis of Acute Occlusive and Chronic Pulmonary Embolism on CT. Int J Angiol. 2024 Jun 5;33(2):132-133. doi: 10.1055/s-0044-1786745. PMID: 38846995; PMCID: PMC11152633.
  3. Donuru A, Torigian DA, Knollmann F. Uncommon Causes of Interlobular Septal Thickening on CT Images and Their Distinguishing Features. Tomography. 2024 Apr 17;10(4):574-608. doi: 10.3390/tomography10040045. PMID: 38668402; PMCID: PMC11054070. 
  4. Talwar AA, Desai AA, McAuliffe PB, Broach RB, Hsu JY, Liu T, Udupa JK, Tong Y, Torigian DA, Fischer JP. Optimal computed tomography-based biomarkers for prediction of incisional hernia formation. Hernia. 2024 Feb;28(1):17-24. doi: 10.1007/s10029-023-02835-7. Epub 2023 Sep 7. PMID: 37676569; PMCID: PMC11235401. 
  5. Song I, Thompson EW, Verma A, MacLean MT, Duda J, Elahi A, Tran R, Raghupathy P, Swago S, Hazim M, Bhattaru A, Schneider C, Vujkovic M, Torigian DA, Kahn CE, Gee JC, Borthakur A, Kripke CM, Carson CC, Carr R, Jehangir Q, Ko YA, Litt H, Rosen M, Mankoff DA, Schnall MD, Shou H, Chirinos J, Damrauer SM, Serper M, Chen J, Rader DJ; Penn Medicine BioBank; Witschey WRT, Sagreiya H. Clinical correlates of CT imaging-derived phenotypes among lean and overweight patients with hepatic steatosis. Sci Rep. 2024 Jan 2;14(1):53. doi: 10.1038/s41598-023-49470-x. PMID: 38167550; PMCID: PMC10761858. 
  6. Dai J, Liu T, Torigian DA, Tong Y, Han S, Nie P, Zhang J, Li R, Xie F, Udupa JK. GA-Net: A geographical attention neural network for the segmentation of body torso tissue composition. Med Image Anal. 2024 Jan;91:102987. doi: 10.1016/j.media.2023.102987. Epub 2023 Sep 29. PMID: 37837691; PMCID: PMC10841506. 
  7. Yao MS, Chae A, MacLean MT, Verma A, Duda J, Gee JC, Torigian DA, Rader D, Kahn CE Jr, Witschey WR, Sagreiya H. SynthA1c: Towards Clinically Interpretable Patient Representations for Diabetes Risk Stratification. Predict Intell Med. 2023 Oct;14277:46-57. doi: 10.1007/978-3-031-46005-0_5. PMID: 38957550; PMCID: PMC11217801. 
  8. Mortazi A, Udupa JK, Odhner D, Tong Y, Torigian DA. Post-acquisition standardization of positron emission tomography images. Front Nucl Med. 2023;3:1210931. doi: 10.3389/fnume.2023.1210931. Epub 2023 Sep 11. PMID: 39015756; PMCID: PMC11251705. 
  9. Shahait M, Usamentiaga R, Tong Y, Sandberg A, Lee DI, Udupa JK, Torigian DA. Periprostatic Adipose Tissue MRI Radiomics-Derived Features Associated with Clinically Significant Prostate Cancer. J Endourol. 2023 Oct;37(10):1156-1161. doi: 10.1089/end.2023.0215. Epub 2023 Aug 31. PMID: 37597206. 
  10. Bobisse S, Bianchi V, Tanyi JL, Sarivalasis A, Missiaglia E, Pétremand R, Benedetti F, Torigian DA, Genolet R, Barras D, Michel A, Mastroyannis SA, Zsiros E, Dangaj Laniti D, Tsourti Z, Stevenson BJ, Iseli C, Levine BL, Speiser DE, Gfeller D, Bassani-Sternberg M, Powell DJ Jr, June CH, Dafni U, Kandalaft LE, Harari A, Coukos G. A phase 1 trial of adoptive transfer of vaccine-primed autologous circulating T cells in ovarian cancer. Nat Cancer. 2023 Oct;4(10):1410-1417. doi: 10.1038/s43018-023-00623-x. Epub 2023 Sep 21. PMID: 37735588. 
  11. Shahait M, Usamentiaga R, Tong Y, Sandberg A, Lee DI, Udupa JK, Torigian DA. MRI-Based Radiomics Analysis of Levator Ani Muscle for Predicting Urine Incontinence after Robot-Assisted Radical Prostatectomy. Diagnostics (Basel). 2023 Sep 11;13(18):2913. doi: 10.3390/diagnostics13182913. PMID: 37761280; PMCID: PMC10528635. 
  12. Anderson MR, Diamond J, Shashaty M, Singer JP, Tong Y, Udupa J, Torigian DA, Palmer S, Lederer DJ, Christie JD, Al-Naamani N. Accuracy and Reproducibility of Automated Measurement of Body Composition: A Lung Transplant Body Composition Cohort Study. Ann Am Thorac Soc. 2023 Sep;20(9):1363-1366. doi: 10.1513/AnnalsATS.202301-061RL. PMID: 37115555; PMCID: PMC10502884. 
  13. Wethington SL, Shah PD, Martin L, Tanyi JL, Latif N, Morgan M, Torigian DA, Rodriguez D, Smith SA, Dean E, Domchek SM, Drapkin R, Shih IM, Brown EJ, Hwang WT, Armstrong DK, Gaillard S, Giuntoli R, Simpkins F. Combination ATR (ceralasertib) and PARP (olaparib) Inhibitor (CAPRI) Trial in Acquired PARP Inhibitor-Resistant Homologous Recombination-Deficient Ovarian Cancer. Clin Cancer Res. 2023 Aug 1;29(15):2800-2807. doi: 10.1158/1078-0432.CCR-22-2444. PMID: 37097611. 
  14. Tong Y, Udupa JK, Chong E, Winchell N, Sun C, Zou Y, Schuster SJ, Torigian DA. Prediction of lymphoma response to CAR T cells by deep learning-based image analysis. PLoS One. 2023 Jul 21;18(7):e0282573. doi: 10.1371/journal.pone.0282573. PMID: 37478073; PMCID: PMC10361488. 
  15. Anderson MR, Diamond J, Shashaty M, Singer JP, Tong Y, Udupa J, Torigian DA, Palmer S, Lederer DJ, Christie JD, Al-Naamani N. Accuracy and Reproducibility of Automated Measurement of Body Composition: A Lung Transplant Body Composition Cohort Study. Ann Am Thorac Soc. 2023 Apr 28. doi: 10.1513/AnnalsATS.202301-061RL. Epub ahead of print. PMID: 37115555.
  16. Pantel AR, Gitto SB, Makvandi M, Kim H, Medvedv S, Weeks JK, Torigian DA, Hsieh CJ, Ferman B, Latif NA, Tanyi JL, Martin LP, Lanzo SM, Liu F, Cao Q, Mills GB, Doot RK, Mankoff DA, Mach RH, Lin LL, Simpkins F. [18F]FluorThanatrace ([18F]FTT) PET Imaging of PARP-Inhibitor Drug-Target Engagement as a Biomarker of Response in Ovarian Cancer, a Pilot Study. Clin Cancer Res. 2023 Apr 14;29(8):1515-1527. doi: 10.1158/1078-0432.CCR-22-1602. PMID: 36441795.
  17. Tong Y, Udupa JK, McDonough JM, Wu C, Sun C, Xie L, Lott C, Clark A, Mayer OH, Anari JB, Torigian DA, Cahill PJ. Assessment of Regional Functional Effects of Surgical Treatment in Thoracic Insufficiency Syndrome via Dynamic Magnetic Resonance Imaging. J Bone Joint Surg Am. 2023 Jan 4;105(1):53-62. doi: 10.2106/JBJS.22.00324. Epub 2022 Dec 15. PMID: 36598475.
  18. Park J, MacLean MT, Lucas AM, Torigian DA, Schneider CV, Cherlin T, Xiao B, Miller JE, Bradford Y, Judy RL; Regeneron Genetics Center; Verma A, Damrauer SM, Ritchie MD, Witschey WR, Rader DJ. Exome-wide association analysis of CT imaging-derived hepatic fat in a medical biobank. Cell Rep Med. 2022 Dec 20;3(12):100855. doi: 10.1016/j.xcrm.2022.100855. Epub 2022 Dec 12. PMID: 36513072; PMCID: PMC9798024.
  19. Udupa JK, Liu T, Jin C, Zhao L, Odhner D, Tong Y, Agrawal V, Pednekar G, Nag S, Kotia T, Goodman M, Wileyto EP, Mihailidis D, Lukens JN, Berman AT, Stambaugh J, Lim T, Chowdary R, Jalluri D, Jabbour SK, Kim S, Reyhan M, Robinson CG, Thorstad WL, Choi JI, Press R, Simone CB 2nd, Camaratta J, Owens S, Torigian DA. Combining natural and artificial intelligence for robust automatic anatomy segmentation: Application in neck and thorax auto-contouring. Med Phys. 2022 Nov;49(11):7118-7149. doi: 10.1002/mp.15854. Epub 2022 Jul 27. PMID: 35833287; PMCID: PMC10087050. This work featured on the cover page of the November 2022 issue of Medical Physics.
  20. McAuliffe PB, Desai AA, Talwar AA, Broach RB, Hsu JY, Serletti JM, Liu T, Tong Y, Udupa JK, Torigian DA, Fischer JP. Preoperative Computed Tomography Morphological Features Indicative of Incisional Hernia Formation After Abdominal Surgery. Ann Surg. 2022 Oct 1;276(4):616-625. doi: 10.1097/SLA.0000000000005583. Epub 2022 Jul 15. PMID: 35837959; PMCID: PMC9484790.
  21. Jin C, Udupa JK, Zhao L, Tong Y, Odhner D, Pednekar G, Nag S, Lewis S, Poole N, Mannikeri S, Govindasamy S, Singh A, Camaratta J, Owens S, Torigian DA. Object recognition in medical images via anatomy-guided deep learning. Med Image Anal. 2022 Oct;81:102527. doi: 10.1016/j.media.2022.102527. Epub 2022 Jun 25. PMID: 35830745.
  22. Choy KR, Sin S, Tong Y, Udupa JK, Luchtenburg DM, Wagshul ME, Arens R, Wootton DM. Upper airway effective compliance during wakefulness and sleep in obese adolescents studied via two-dimensional dynamic MRI and semiautomated image segmentation. J Appl Physiol (1985). 2021;131(2):532-43. doi: 10.1152/japplphysiol.00839.2020. PubMed PMID: 34080921; PMCID: PMC8409921.
  23. Li J, Udupa JK, Odhner D, Tong Y, Torigian DA. SOMA: Subject-, object-, and modality-adapted precision atlas approach for automatic anatomy recognition and delineation in medical images. Med Phys. 2021;48(12):7806-25. doi: 10.1002/mp.15308. PubMed PMID: 34668207; PMCID: PMC8678400.
  24. Bitners AC, Sin S, Agrawal S, Lee S, Udupa JK, Tong Y, Wootton DM, Choy KR, Wagshul ME, Arens R. Effect of sleep on upper airway dynamics in obese adolescents with obstructive sleep apnea syndrome. Sleep. 2020 Oct 13;43(10):zsaa071. doi: 10.1093/sleep/zsaa071. PMID: 32280981; PMCID: PMC7551304.
  25. Zaidi H, Alavi A, Torigian DA. Recent Advances in Imaging with PET, Computed Tomography, and MR Techniques. PET Clin. 2020 Oct;15(4):xv-xvi. doi: 10.1016/j.cpet.2020.08.002. PMID: 32888550.
  26. Xu G, Cao H, Udupa JK, Tong Y, Torigian DA. DiSegNet: A deep dilated convolutional encoder-decoder architecture for lymph node segmentation on PET/CT images. Comput Med Imaging Graph. 2021 Mar;88:101851. doi:10.1016/j.compmedimag.2020.101851. Epub 2020 Dec 29. PMID: 33465588.
  27. Agrawal V, Udupa J, Tong Y, Torigian D. BRR-Net: A tandem architectural CNN-RNN for automatic body region localization in CT images. Med Phys. 2020 Oct;47(10):5020-5031. doi: 10.1002/mp.14439. Epub 2020 Aug 20. PMID: 32761899.
  28. Al-Naamani N, Pan HM, Anderson MR, Torigian DA, Tong Y, Oyster M, Porteous MK, Palmer S, Arcasoy SM, Diamond JM, Udupa JK, Christie JD, Lederer DJ, Kawut SM. Thoracic Visceral Adipose Tissue Area and Pulmonary Hypertension in Lung Transplant Candidates. The Lung Transplant Body Composition Study. Ann Am Thorac Soc. 2020 Nov;17(11):1393-1400. doi: 10.1513/AnnalsATS.202003-247OC. PMID: 32530703; PMCID: PMC7640728.
  29. Anderson MR, Easthausen I, Gallagher G, Udupa J, Tong Y, Torigian D, Diamond JM, Porteous MK, Palmer SM, Snyder LD, Benvenuto L, Aversa M, Arcasoy S, Greenland JR, Hays SR, Kukreja J, Cantu E, Kim JS, Gallagher D, Baldwin MR, Barr RG, Lederer DJ, Christie JD, Singer JP. Skeletal muscle adiposity and outcomes in candidates for lung transplantation: a lung transplant body composition cohort study. Thorax. 2020 Sep;75(9):801-804. doi: 10.1136/thoraxjnl-2019-214461. Epub 2020 Jun 1. PMID: 32482837; PMCID: PMC7888552.
  30. Xu G, Udupa JK, Tong Y, Odhner D, Cao H, Torigian DA. AAR-LN-DQ: Automatic anatomy recognition based disease quantification in thoracic lymph node zones via FDG PET/CT images without Nodal Delineation. Med Phys. 2020 Aug;47(8):3467-3484. doi: 10.1002/mp.14240. Epub 2020 Jun 15. PMID: 32418221.
  31. Liu T, Pan J, Torigian DA, Xu P, Miao Q, Tong Y, Udupa JK. ABCNet: A new efficient 3D dense-structure network for segmentation and analysis of body tissue composition on body-torso-wide CT images. Med Phys. 2020 Jul;47(7):2986-2999. doi: 10.1002/mp.14141. Epub 2020 Apr 21. PMID: 32170754.
  32. Hao Y, Udupa JK, Tong Y, Wu C, Li H, McDonough JM, Lott C, Qiu C, Galagedera N, Anari JB, Torigian DA, Cahill PJ. OFx: A method of 4D image construction from free-breathing non-gated MRI slice acquisitions of the thorax via optical flux. Med Image Anal. 2021 Aug;72:102088. doi: 10.1016/j.media.2021.102088. Epub 2021 Apr 25. PMID: 34052519; PMCID: PMC8316349.
  33. Tanyi JL, Chiang CL, Chiffelle J, Thierry AC, Baumgartener P, Huber F, Goepfert C, Tarussio D, Tissot S, Torigian DA, Nisenbaum HL, Stevenson BJ, Guiren HF, Ahmed R, Huguenin-Bergenat AL, Zsiros E, Bassani-Sternberg M, Mick R, Powell DJ Jr, Coukos G, Harari A, Kandalaft LE. Author Correction: Personalized cancer vaccine strategy elicits polyfunctional T cells and demonstrates clinical benefits in ovarian cancer. NPJ Vaccines. 2021 May 4;6(1):68. doi:10.1038/s41541-021-00332-5. Erratum for: NPJ Vaccines. 2021 Mar 15;6(1):36. PMID: 33947868; PMCID: PMC8096937.
  34. Tanyi JL, Chiang CL, Chiffelle J, Thierry AC, Baumgartener P, Huber F, Goepfert C, Tarussio D, Tissot S, Torigian DA, Nisenbaum HL, Stevenson BJ, Guiren HF, Ahmed R, Huguenin-Bergenat AL, Zsiros E, Bassani-Sternberg M, Mick R, Powell DJ Jr, Coukos G, Harari A, Kandalaft LE. Personalized cancer vaccine strategy elicits polyfunctional T cells and demonstrates clinical benefits in ovarian cancer. NPJ Vaccines. 2021 Mar 15;6(1):36. doi: 10.1038/s41541-021-00297-5. Erratum in: NPJ Vaccines. 2021 May 4;6(1):68. PMID: 33723260; PMCID: PMC7960755.
  35. Li J, Udupa JK, Tong Y, Wang L, Torigian DA. Segmentation evaluation with sparse ground truth data: Simulating true segmentations as perfect/imperfect as those generated by humans. Med Image Anal. 2021 Apr;69:101980. doi: 10.1016/j.media.2021.101980. Epub 2021 Jan 26. PMID: 33588116; PMCID:PMC7933105.
  36. MacLean MT, Jehangir Q, Vujkovic M, Ko YA, Litt H, Borthakur A, Sagreiya H, Rosen M, Mankoff DA, Schnall MD, Shou H, Chirinos J, Damrauer SM, Torigian DA, Carr R, Rader DJ, Witschey WR. Quantification of abdominal fat from computed tomography using deep learning and its association with electronic health records in an academic biobank. J Am Med Inform Assoc. 2021 Jun 12;28(6):1178-1187. doi: 10.1093/jamia/ocaa342. PMID: 33576413.
  37. Auld SC, Kornfeld H, Maenetje P, Mlotshwa M, Chase W, Vangu MD, Torigian DA, Wallis RS, Churchyard G, Bisson GP. Pulmonary restriction predicts long-term pulmonary impairment in people with HIV and tuberculosis. BMC Pulm Med. 2021 Jan 7;21(1):19. doi: 10.1186/s12890-020-01368-4. PMID: 33413293; PMCID: PMC7791797.
  38. Tong Y, Udupa JK, McDonough JM, Wu C, Sun C, Qiu C, Lott C, Galagedera N, Anari JB, Mayer OH, Torigian DA, Cahill PJ. Thoracic Quantitative Dynamic MRI to Understand Developmental Changes in Normal Ventilatory Dynamics. Chest. 2021 Feb;159(2):712-723. doi: 10.1016/j.chest.2020.07.066. Epub 2020 Aug 6. PMID: 32768456; PMCID: PMC7856528.
  39. Galperin-Aizenberg M, Katz S, Shankla V, Wileyto EP, Gefter W, Dougherty L, Torigian DA, Barbosa E Jr. Preliminary Assessment of an Optical Flow Method (OFM) for Nonrigid Registration and Temporal Subtraction (TS) of Serial CT Examinations to Facilitate Evaluation of Interval Change in Metastatic Lung Nodules. Curr Probl Diagn Radiol. 2021 May-Jun;50(3):344-350. doi: 10.1067/j.cpradiol.2020.02.005. Epub 2020 Mar 2. PMID: 32249018.
  40. Patel A, Roshkovan L, McNulty S, Alley E, Torigian DA, Nachiappan AC, Galperin-Aizenberg M, Barbosa EM Jr, DiRienzi J, Berger I, Khalid U, Haas AR, Singhal S, Wileyto EP, Cengel KA, Katz SI. Delayed-Phase Enhancement for Evaluation of Malignant Pleural Mesothelioma on Computed Tomography: A Prospective Cohort Study. Clin Lung Cancer. 2021 May;22(3):210-217.e1. doi:10.1016/j.cllc.2020.06.002. Epub 2020 Jun 14. PMID: 32693945. 
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