IPA Group Publications

2024

High-resolution extracellular pH imaging of liver cancer with multiparametric MR using Deep Image Prior.Dong S, Shewarega A, Chapiro J, Cai Z, Hyder F, Coman D, Duncan JS. NMR Biomed. 2024 Mar 15; 2024 Mar 15. PMID: 38488205.
Multicenter Quantification of Radiation Exposure and Associated Risks for Prostatic Artery Embolization in 1476 Patients.Ayyagari R, Rahman SZ, Grizzard K, Mustafa A, Staib LH, Makkia RS, Bhatia S, Bilhim T, Carnevale FC, Davis C, Fischman A, Isaacson A, McClure T, McWilliams J, Nutting C, Richardson A, Salem R, Sapoval M, Yu H. Radiology. 2024 Mar. PMID: 38441098.
Effect of Incomplete Cryoablation and Matrix Metalloproteinase Inhibition on Intratumoral CD8(+) T-Cell Infiltration in Murine Hepatocellular Carcinoma.Shewarega A, Santana JG, Nam D, Berz A, Tefera J, Kahl V, Mishra SK, Coman D, Duncan J, Roberts SJ, Wetter A, Madoff DC, Chapiro J. Radiology. 2024 Feb. PMID: 38349244.
A Physics-Based Algorithm to Universally Standardize Routinely Obtained Clinical T(2)-Weighted Images.Elsaid NMH, Tagare HD, Galiana G. Acad Radiol. 2024 Feb; 2023 Jul 6. PMID: 37407374.
Multimodal measures of spontaneous brain activity reveal both common and divergent patterns of cortical functional organization.Vafaii H, Mandino F, Desrosiers-Grégoire G, O'Connor D, Markicevic M, Shen X, Ge X, Herman P, Hyder F, Papademetris X, Chakravarty M, Crair MC, Constable RT, Lake EMR, Pessoa L. Nat Commun. 2024 Jan 3; 2024 Jan 3. PMID: 38172111.
Performance and reliability assessment of a lower dose, task-based scoliosis radiography protocol in pediatric patients.Al-Dasuqi K, Taylor E, Ehrlich L, Cooperman D, Socci A, Tuason D, Hoerner M, Staib L, Silva CT. Pediatr Radiol. 2024 Jan; 2023 Nov 27. PMID: 38010426.
Deferral of Estimated Glomerular Filtration Rate Testing Before Contrast-Enhanced CT in Low-Risk Emergency Department Patients: Assessment of Safety and Impact on Throughput.Gunabushanam G, Asch D, van Luling J, Kuehne A, Alkukhun A, Staib L, Venkatesh A, Pahade JK. J Am Coll Radiol. 2024 Jan; 2023 Nov 6. PMID: 37939813.

2023

Brain Registration and Evaluation for Zebrafish (BREEZE)-mapping: A pipeline for whole-brain structural and activity analyses.Jin DS, Neelakantan U, Lacadie CM, Chen T, Rooney B, Liu Y, Wu W, Wang Z, Papademetris X, Hoffman EJ. STAR Protoc. 2023 Dec 15; 2023 Oct 26. PMID: 37897734.
FedFTN: Personalized federated learning with deep feature transformation network for multi-institutional low-count PET denoising.Zhou B, Xie H, Liu Q, Chen X, Guo X, Feng Z, Hou J, Zhou SK, Li B, Rominger A, Shi K, Duncan JS, Liu C. Med Image Anal. 2023 Dec; 2023 Oct 6. PMID: 37827110.
A Multiclass Radiomics Method-Based WHO Severity Scale for Improving COVID-19 Patient Assessment and Disease Characterization From CT Scans.Henao JAG, Depotter A, Bower DV, Bajercius H, Todorova PT, Saint-James H, de Mortanges AP, Barroso MC, He J, Yang J, You C, Staib LH, Gange C, Ledda RE, Caminiti C, Silva M, Cortopassi IO, Dela Cruz CS, Hautz W, Bonel HM, Sverzellati N, Duncan JS, Reyes M, Poellinger A. Invest Radiol. 2023 Dec 1; 2023 Jul 27. PMID: 37493348.
HIV-1 Env trimers asymmetrically engage CD4 receptors in membranes.Li W, Qin Z, Nand E, Grunst MW, Grover JR, Bess JW Jr, Lifson JD, Zwick MB, Tagare HD, Uchil PD, Mothes W. Nature. 2023 Nov; 2023 Nov 22. PMID: 37993716.
Copy Number Variation Informs fMRI-based Prediction of Autism Spectrum Disorder.Dvornek NC, Sullivan C, Duncan JS, Gupta AR. Mach Learn Clin Neuroimaging (2023). 2023 Oct; 2023 Oct 1. PMID: 38371906.
Cross-Attention for Improved Motion Correction in Brain PET.Cai Z, Zeng T, Lieffrig EV, Zhang J, Chen F, Toyonaga T, You C, Xin J, Zheng N, Lu Y, Duncan JS, Onofrey JA. Mach Learn Clin Neuroimaging (2023). 2023 Oct; 2023 Oct 1. PMID: 38174216.
Multiaxial pressure-strain analysis of regional myocardial work in the setting of graded coronary stenoses and dobutamine stress.Stendahl JC, Liu Z, Boutagy NE, Parajuli N, Lu A, Alkhalil I, Lin BA, Duncan JS, Sinusas AJ. Am J Physiol Heart Circ Physiol. 2023 Sep 1; 2023 Jul 7. PMID: 37417870.
Improvement in cardiac function and regional LV strain following intramyocardial injection of a theranostic hydrogel early postmyocardial infarction in a porcine model.Avendaño R, Midgett D, Melvinsdottir I, Thorn SL, Uman S, Pickell Z, Lee SR, Liu Z, Mamarian M, Duncan JS, Spinale FG, Burdick JA, Sinusas AJ. J Appl Physiol (1985). 2023 Aug 1; 2023 Jun 15. PMID: 37318987.
DuSFE: Dual-Channel Squeeze-Fusion-Excitation co-attention for cross-modality registration of cardiac SPECT and CT.Chen X, Zhou B, Xie H, Guo X, Zhang J, Duncan JS, Miller EJ, Sinusas AJ, Onofrey JA, Liu C. Med Image Anal. 2023 Aug; 2023 May 16. PMID: 37216735.
New measures of anisotropy of cryo-EM maps.Vilas JL, Tagare HD. Nat Methods. 2023 Jul; 2023 May 29. PMID: 37248387.
Bootstrapping Semi-supervised Medical Image Segmentation with Anatomical-Aware Contrastive Distillation.You C, Dai W, Min Y, Staib L, Duncan JS. Inf Process Med Imaging. 2023 Jun; 2023 Jun 8. PMID: 37409056.
Clustering of KOR PET images separates people with AUD into distinct responses to naltrexone.Hoye J, Key J, de Laat B, Cosgrove KP, Krishnan-Sarin S, Papademetris X, Morris ED. Brain Imaging Behav. 2023 Jun; 2023 Jan 25. PMID: 36695971.
Predicting tumor recurrence on baseline MR imaging in patients with early-stage hepatocellular carcinoma using deep machine learning.Kucukkaya AS, Zeevi T, Chai NX, Raju R, Haider SP, Elbanan M, Petukhova-Greenstein A, Lin M, Onofrey J, Nowak M, Cooper K, Thomas E, Santana J, Gebauer B, Mulligan D, Staib L, Batra R, Chapiro J. Sci Rep. 2023 May 10; 2023 May 10. PMID: 37165035.
Multimodal measures of spontaneous brain activity reveal both common and divergent patterns of cortical functional organization.Vafaii H, Mandino F, Desrosiers-Grégoire G, O'Connor D, Shen X, Ge X, Herman P, Hyder F, Papademetris X, Chakravarty M, Crair MC, Constable RT, Lake EM, Pessoa L. Res Sq. 2023 Apr 26; 2023 Apr 26. PMID: 37162818.
INTEGRATING PROSTATE SPECIFIC ANTIGEN DENSITY BIOMARKER INTO DEEP LEARNING PROSTATE MRI LESION SEGMENTATION MODELS.Zhong J, Staib LH, Venkataraman R, Onofrey JA. Proc IEEE Int Symp Biomed Imaging. 2023 Apr; 2023 Sep 1. PMID: 38090633.
RAPID BRAIN MENINGES SURFACE RECONSTRUCTION WITH LAYER TOPOLOGY GUARANTEE.Duan P, Xue Y, Han S, Zuo L, Carass A, Bernhard C, Hays S, Calabresi PA, Resnick SM, Duncan JS, Prince JL. Proc IEEE Int Symp Biomed Imaging. 2023 Apr; 2023 Sep 1. PMID: 37990735.
Deep Learning for Breast MRI Style Transfer with Limited Training Data.Cao S, Konz N, Duncan J, Mazurowski MA. J Digit Imaging. 2023 Apr; 2022 Dec 21. PMID: 36544066.
HALO: A software tool for real-time head alignment in the MR scanner.Zhao Z, Galiana G, Zillo C, Camarro T, Qiu M, Papademetris X, Hampson M. Magn Reson Med. 2023 Apr; 2022 Nov 25. PMID: 36426774.
High-throughput functional analysis of autism genes in zebrafish identifies convergence in dopaminergic and neuroimmune pathways.Weinschutz Mendes H, Neelakantan U, Liu Y, Fitzpatrick SE, Chen T, Wu W, Pruitt A, Jin DS, Jamadagni P, Carlson M, Lacadie CM, Enriquez KD, Li N, Zhao D, Ijaz S, Sakai C, Szi C, Rooney B, Ghosh M, Nwabudike I, Gorodezky A, Chowdhury S, Zaheer M, McLaughlin S, Fernandez JM, Wu J, Eilbott JA, Vander Wyk B, Rihel J, Papademetris X, Wang Z, Hoffman EJ. Cell Rep. 2023 Mar 28; 2023 Mar 17. PMID: 36933215.
Federated Transfer Learning for Low-dose PET Denoising: A Pilot Study with Simulated Heterogeneous Data.Zhou B, Miao T, Mirian N, Chen X, Xie H, Feng Z, Guo X, Li X, Zhou SK, Duncan JS, Liu C. IEEE Trans Radiat Plasma Med Sci. 2023 Mar; 2022 Jul 27. PMID: 37789946.
Co-attention spatial transformer network for unsupervised motion tracking and cardiac strain analysis in 3D echocardiography.Ahn SS, Ta K, Thorn SL, Onofrey JA, Melvinsdottir IH, Lee S, Langdon J, Sinusas AJ, Duncan JS. Med Image Anal. 2023 Feb; 2022 Dec 9. PMID: 36525845.
Operator Learning Curve for Prostatic Artery Embolization and Its Impact on Outcomes in 296 Patients.Powell T, Rahman S, Staib L, Bhatia S, Ayyagari R. Cardiovasc Intervent Radiol. 2023 Feb; 2022 Dec 1. PMID: 36456689.
Machine Learning Models for Prediction of Posttreatment Recurrence in Early-Stage Hepatocellular Carcinoma Using Pretreatment Clinical and MRI Features: A Proof-of-Concept Study.Iseke S, Zeevi T, Kucukkaya AS, Raju R, Gross M, Haider SP, Petukhova-Greenstein A, Kuhn TN, Lin M, Nowak M, Cooper K, Thomas E, Weber MA, Madoff DC, Staib L, Batra R, Chapiro J. AJR Am J Roentgenol. 2023 Feb; 2022 Aug 17. PMID: 35975886.

2022

Class-Aware Adversarial Transformers for Medical Image Segmentation.You C, Zhao R, Liu F, Dong S, Chinchali S, Topcu U, Staib L, Duncan JS. Adv Neural Inf Process Syst. 2022 Dec. PMID: 37533756.
High-resolution cortical parcellation based on conserved brain landmarks for localization of multimodal data to the nearest centimeter.McGrath H, Zaveri HP, Collins E, Jafar T, Chishti O, Obaid S, Ksendzovsky A, Wu K, Papademetris X, Spencer DD. Sci Rep. 2022 Nov 5; 2022 Nov 5. PMID: 36335146.
Dual-domain self-supervised learning for accelerated non-Cartesian MRI reconstruction.Zhou B, Schlemper J, Dey N, Mohseni Salehi SS, Sheth K, Liu C, Duncan JS, Sofka M. Med Image Anal. 2022 Oct; 2022 Jul 18. PMID: 35926336.
Multiparameter analysis of timelapse imaging reveals kinetics of megakaryocytic erythroid progenitor clonal expansion and differentiation.Scanlon VM, Thompson EN, Lawton BR, Kochugaeva M, Ta K, Mayday MY, Xavier-Ferrucio J, Kang E, Eskow NM, Lu YC, Kwon N, Laumas A, Cenci M, Lawrence K, Barden K, Larsuel ST, Reed FE, Peña-Carmona G, Ubbelohde A, Lee JP, Boobalan S, Oppong Y, Anderson R, Maynard C, Sahirul K, Lajeune C, Ivathraya V, Addy T, Sanchez P, Holbrook C, Van Ho AT, Duncan JS, Blau HM, Levchenko A, Krause DS. Sci Rep. 2022 Sep 28; 2022 Sep 28. PMID: 36171423.
Atlas-based Semantic Segmentation of Prostate Zones.Zhang J, Venkataraman R, Staib LH, Onofrey JA. Med Image Comput Comput Assist Interv. 2022 Sep; 2022 Sep 16. PMID: 38084296.
Momentum Contrastive Voxel-wise Representation Learning for Semi-supervised Volumetric Medical Image Segmentation.You C, Zhao R, Staib L, Duncan JS. Med Image Comput Comput Assist Interv. 2022 Sep; 2022 Sep 16. PMID: 37465615.
Incremental Learning Meets Transfer Learning: Application to Multi-site Prostate MRI Segmentation.You C, Xiang J, Su K, Zhang X, Dong S, Onofrey J, Staib L, Duncan JS. Distrib Collab Fed Learn Afford AI Healthc Resour Div Glob Health (2022). 2022 Sep; 2022 Oct 7. PMID: 37415747.
Prediction of Adverse Pathology at Radical Prostatectomy in Grade Group 2 and 3 Prostate Biopsies Using Machine Learning.Paulson N, Zeevi T, Papademetris M, Leapman MS, Onofrey JA, Sprenkle PC, Humphrey PA, Staib LH, Levi AW. JCO Clin Cancer Inform. 2022 Sep. PMID: 36179281.
Cryoablation of Venous Malformations: A Systematic Review.Fish A, Moushey A, Chan SM, Staib L, Marino A, Schlachter T. J Vasc Interv Radiol. 2022 Aug; 2022 Apr 22. PMID: 35469956.
MR Imaging Biomarkers for the Prediction of Outcome after Radiofrequency Ablation of Hepatocellular Carcinoma: Qualitative and Quantitative Assessments of the Liver Imaging Reporting and Data System and Radiomic Features.Petukhova-Greenstein A, Zeevi T, Yang J, Chai N, DiDomenico P, Deng Y, Ciarleglio M, Haider SP, Onyiuke I, Malpani R, Lin M, Kucukkaya AS, Gottwald LA, Gebauer B, Revzin M, Onofrey J, Staib L, Gunabushanam G, Taddei T, Chapiro J. J Vasc Interv Radiol. 2022 Jul; 2022 Apr 20. PMID: 35460887.
Identifying clinically applicable machine learning algorithms for glioma segmentation: recent advances and discoveries.Tillmanns N, Lum AE, Cassinelli G, Merkaj S, Verma T, Zeevi T, Staib L, Subramanian H, Bahar RC, Brim W, Lost J, Jekel L, Brackett A, Payabvash S, Ikuta I, Lin M, Bousabarah K, Johnson MH, Cui J, Malhotra A, Omuro A, Turowski B, Aboian MS. Neurooncol Adv. 2022 Jan-Dec; 2022 Jun 14. PMID: 36071926.
Machine Learning Tools for Image-Based Glioma Grading and the Quality of Their Reporting: Challenges and Opportunities.Merkaj S, Bahar RC, Zeevi T, Lin M, Ikuta I, Bousabarah K, Cassinelli Petersen GI, Staib L, Payabvash S, Mongan JT, Cha S, Aboian MS. Cancers (Basel). 2022 May 25; 2022 May 25. PMID: 35681603.
Cryo-EM structure of the plant 26S proteasome.Kandolf S, Grishkovskaya I, Belačić K, Bolhuis DL, Amann S, Foster B, Imre R, Mechtler K, Schleiffer A, Tagare HD, Zhong ED, Meinhart A, Brown NG, Haselbach D. Plant Commun. 2022 May 9; 2022 Mar 11. PMID: 35576154.
Machine Learning Models for Classifying High- and Low-Grade Gliomas: A Systematic Review and Quality of Reporting Analysis.Bahar RC, Merkaj S, Cassinelli Petersen GI, Tillmanns N, Subramanian H, Brim WR, Zeevi T, Staib L, Kazarian E, Lin M, Bousabarah K, Huttner AJ, Pala A, Payabvash S, Ivanidze J, Cui J, Malhotra A, Aboian MS. Front Oncol. 2022; 2022 Apr 22. PMID: 35530302.
Machine Learning Applications for Differentiation of Glioma from Brain Metastasis-A Systematic Review.Jekel L, Brim WR, von Reppert M, Staib L, Cassinelli Petersen G, Merkaj S, Subramanian H, Zeevi T, Payabvash S, Bousabarah K, Lin M, Cui J, Brackett A, Mahajan A, Omuro A, Johnson MH, Chiang VL, Malhotra A, Scheffler B, Aboian MS. Cancers (Basel). 2022 Mar 8; 2022 Mar 8. PMID: 35326526.
Quantitative Automated Segmentation of Lipiodol Deposits on Cone-Beam CT Imaging Acquired during Transarterial Chemoembolization for Liver Tumors: A Deep Learning Approach.Malpani R, Petty CW, Yang J, Bhatt N, Zeevi T, Chockalingam V, Raju R, Petukhova-Greenstein A, Santana JG, Schlachter TR, Madoff DC, Chapiro J, Duncan J, Lin M. J Vasc Interv Radiol. 2022 Mar; 2021 Dec 16. PMID: 34923098.
Using Adversarial Images to Assess the Robustness of Deep Learning Models Trained on Diagnostic Images in Oncology.Joel MZ, Umrao S, Chang E, Choi R, Yang DX, Duncan JS, Omuro A, Herbst R, Krumholz HM, Aneja S. JCO Clin Cancer Inform. 2022 Feb. PMID: 35271304.
Steerable Near-Quadrature Filter Pairs in Three Dimensions.Tang TM, Tagare HD. SIAM J Imaging Sci. 2022; 2022 May 26. PMID: 36425343.
Simultaneous Segmentation and Motion Estimation of Left Ventricular Myocardium in 3D Echocardiography Using Multi-task Learning.Ta K, Ahn SS, Stendahl JC, Langdon J, Sinusas AJ, Duncan JS. Stat Atlases Comput Models Heart. 2022; 2022 Jan 14. PMID: 35759335.
DuDoDR-Net: Dual-domain data consistent recurrent network for simultaneous sparse view and metal artifact reduction in computed tomography.Zhou B, Chen X, Zhou SK, Duncan JS, Liu C. Med Image Anal. 2022 Jan; 2021 Oct 29. PMID: 34758443.
Cumulative diagnostic imaging radiation exposure in premature neonates.Khattab M, Hagan J, Staib LH, Mustafa A, Goodman TR. J Neonatal Perinatal Med. 2022. PMID: 33843704.

2021

Self-normalized Classification of Parkinson's Disease DaTscan Images.Zhou Y, Tagare HD. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2021 Dec. PMID: 35425663.
Hierarchical MAP Denoising of Longitudinal Hamilton Depression Rating Scores.Koss J, DeLorenzo C, Tagare HD. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2021 Dec. PMID: 35419210.
BrainGNN: Interpretable Brain Graph Neural Network for fMRI Analysis.Li X, Zhou Y, Dvornek N, Zhang M, Gao S, Zhuang J, Scheinost D, Staib LH, Ventola P, Duncan JS. Med Image Anal. 2021 Dec; 2021 Sep 12. PMID: 34655865.
The cavernous carotid inferolateral trunk and persistent primitive maxillary arteries: analysis of dissected arterially injected fetal specimens and high-resolution micro-CT of the dog's anastomotic arteries.Kier EL, Conlogue GJ, Staib LH. Surg Radiol Anat. 2021 Dec; 2021 Jun 6. PMID: 34091716.
Identifying enhancement-based staging markers on baseline MRI in patients with colorectal cancer liver metastases undergoing intra-arterial tumor therapy.Ghani MA, Fereydooni A, Chen E, Letzen B, Laage-Gaupp F, Nezami N, Deng Y, Gan G, Thakur V, Lin M, Papademetris X, Schernthaner RE, Huber S, Chapiro J, Hong K, Georgiades C. Eur Radiol. 2021 Dec; 2021 Jun 1. PMID: 34061209.
Voiding and Storage Domain-Specific Symptom Score Outcomes After Prostate Artery Embolization for Lower Urinary Tract Symptoms and Urinary Retention.Powell T, Staib L, Liu B, Bhatia S, Chai T, Ayyagari R. Urology. 2021 Oct; 2021 May 4. PMID: 33961894.
Multi-frame Attention Network for Left Ventricle Segmentation in 3D Echocardiography.Ahn SS, Ta K, Thorn S, Langdon J, Sinusas AJ, Duncan JS. Med Image Comput Comput Assist Interv. 2021 Sep-Oct; 2021 Sep 21. PMID: 34729554.
Creating a Radiology Call Center Hotline and "HOT" Sites: Centralizing Radiology Questions and Cohorting Out-patient Care During the COVID-19 Pandemic.Jang B, Facchini D, Staib L, Fernandez A, Pye S, Goodman RT, Granucci C, Nardecchia N, Pahade JK. Curr Probl Diagn Radiol. 2021 Sep-Oct; 2020 Sep 26. PMID: 33036812.
Prognostic Value of Radiotracer-Based Perfusion Imaging in Critical Limb Ischemia Patients Undergoing Lower Extremity Revascularization.Chou TH, Alvelo JL, Janse S, Papademetris X, Sumpio BE, Mena-Hurtado C, Sinusas AJ, Stacy MR. JACC Cardiovasc Imaging. 2021 Aug; 2020 Nov 18. PMID: 33221224.
Author Correction: Simultaneous cortex-wide fluorescence Ca(2+) imaging and whole-brain fMRI.Lake EMR, Ge X, Shen X, Herman P, Hyder F, Cardin JA, Higley MJ, Scheinost D, Papademetris X, Crair MC, Constable RT. Nat Methods. 2021 Jul. PMID: 34163088.
Anatomy-guided multimodal registration by learning segmentation without ground truth: Application to intraprocedural CBCT/MR liver segmentation and registration.Zhou B, Augenfeld Z, Chapiro J, Zhou SK, Liu C, Duncan JS. Med Image Anal. 2021 Jul; 2021 Mar 21. PMID: 33823397.
Deep learning-assisted differentiation of pathologically proven atypical and typical hepatocellular carcinoma (HCC) versus non-HCC on contrast-enhanced MRI of the liver.Oestmann PM, Wang CJ, Savic LJ, Hamm CA, Stark S, Schobert I, Gebauer B, Schlachter T, Lin M, Weinreb JC, Batra R, Mulligan D, Zhang X, Duncan JS, Chapiro J. Eur Radiol. 2021 Jul; 2021 Jan 6. PMID: 33409782.
Current state of radiology report release in electronic patient portals.Holder J, Tocino I, Facchini D, Nardecchia N, Staib L, Crawley D, Pahade JK. Clin Imaging. 2021 Jun; 2021 Jan 5. PMID: 33429142.
A review of deep learning in medical imaging: Imaging traits, technology trends, case studies with progress highlights, and future promises.Zhou SK, Greenspan H, Davatzikos C, Duncan JS, van Ginneken B, Madabhushi A, Prince JL, Rueckert D, Summers RM. Proc IEEE Inst Electr Electron Eng. 2021 May; 2021 Feb 26. PMID: 37786449.
Special issue on MICCAI 2019.Staib LH, Shi P. Med Image Anal. 2021 May; 2021 Mar 13. PMID: 33773295.
SHAPE-REGULARIZED UNSUPERVISED LEFT VENTRICULAR MOTION NETWORK WITH SEGMENTATION CAPABILITY IN 3D+TIME ECHOCARDIOGRAPHY.Ta K, Ahn SS, Stendahl JC, Sinusas AJ, Duncan JS. Proc IEEE Int Symp Biomed Imaging. 2021 Apr; 2021 May 25. PMID: 34168721.
Use of Artificial Intelligence in Non-Oncologic Interventional Radiology: Current State and Future Directions.Malpani R, Petty CW, Bhatt N, Staib LH, Chapiro J. Dig Dis Interv. 2021; 2021 Jul 17. PMID: 35005333.
Automated detection and delineation of hepatocellular carcinoma on multiphasic contrast-enhanced MRI using deep learning.Bousabarah K, Letzen B, Tefera J, Savic L, Schobert I, Schlachter T, Staib LH, Kocher M, Chapiro J, Lin M. Abdom Radiol (NY). 2021 Jan; 2020 Jun 4. PMID: 32500237.

2020

Simultaneous cortex-wide fluorescence Ca(2+) imaging and whole-brain fMRI.Lake EMR, Ge X, Shen X, Herman P, Hyder F, Cardin JA, Higley MJ, Scheinost D, Papademetris X, Crair MC, Constable RT. Nat Methods. 2020 Dec; 2020 Nov 2. PMID: 33139894.
Automated feature quantification of Lipiodol as imaging biomarker to predict therapeutic efficacy of conventional transarterial chemoembolization of liver cancer.Stark S, Wang C, Savic LJ, Letzen B, Schobert I, Miszczuk M, Murali N, Oestmann P, Gebauer B, Lin M, Duncan J, Schlachter T, Chapiro J. Sci Rep. 2020 Oct 22; 2020 Oct 22. PMID: 33093524.
A Semi-supervised Joint Network for Simultaneous Left Ventricular Motion Tracking and Segmentation in 4D Echocardiography.Ta K, Ahn SS, Stendahl JC, Sinusas AJ, Duncan JS. Med Image Comput Comput Assist Interv. 2020 Oct; 2020 Sep 29. PMID: 33094292.
Pooling Regularized Graph Neural Network for fMRI Biomarker Analysis.Li X, Zhou Y, Dvornek NC, Zhang M, Zhuang J, Ventola P, Duncan JS. Med Image Comput Comput Assist Interv. 2020 Oct; 2020 Sep 29. PMID: 33043324.
Idarubicin-Loaded ONCOZENE Drug-Eluting Bead Chemoembolization in a Rabbit Liver Tumor Model: Investigating Safety, Therapeutic Efficacy, and Effects on Tumor Microenvironment.Borde T, Laage Gaupp F, Geschwind JF, Savic LJ, Miszczuk M, Rexha I, Adam L, Walsh JJ, Huber S, Duncan JS, Peters DC, Sinusas A, Schlachter T, Gebauer B, Hyder F, Coman D, van Breugel JMM, Chapiro J. J Vasc Interv Radiol. 2020 Oct; 2020 Jul 17. PMID: 32684417.
Multi-site fMRI analysis using privacy-preserving federated learning and domain adaptation: ABIDE results.Li X, Gu Y, Dvornek N, Staib LH, Ventola P, Duncan JS. Med Image Anal. 2020 Oct; 2020 Jul 2. PMID: 32679533.
Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures.Melero R, Sorzano COS, Foster B, Vilas JL, Martínez M, Marabini R, Ramírez-Aportela E, Sanchez-Garcia R, Herreros D, Del Caño L, Losana P, Fonseca-Reyna YC, Conesa P, Wrapp D, Chacon P, McLellan JS, Tagare HD, Carazo JM. IUCrJ. 2020 Sep 29; 2020 Sep 29. PMID: 33063791.
Predicting Infiltrative Hepatocellular Carcinoma Patient Outcome Post-TACE: MR Bias Field Correction Effect on 3D-quantitative Image Analysis.Liu C, Smolka S, Papademetris X, Minh DD, Gan G, Deng Y, Lin M, Chapiro J, Wang X, Georgiades C, Hong K. J Clin Transl Hepatol. 2020 Sep 28; 2020 Aug 18. PMID: 33083252.
Molecular MRI of the Immuno-Metabolic Interplay in a Rabbit Liver Tumor Model: A Biomarker for Resistance Mechanisms in Tumor-targeted Therapy?Savic LJ, Doemel LA, Schobert IT, Montgomery RR, Joshi N, Walsh JJ, Santana J, Pekurovsky V, Zhang X, Lin M, Adam L, Boustani A, Duncan J, Leng L, Bucala RJ, Goldberg SN, Hyder F, Coman D, Chapiro J. Radiology. 2020 Sep; 2020 Jul 7. PMID: 32633675.
Impact of Radiologist-Driven Change-Order Requests on Outpatient CT and MRI Examinations.Pourjabbar S, Cavallo JJ, Arango J, Tocino I, Staib LH, Imanzadeh A, Forman HP, Pahade JK. J Am Coll Radiol. 2020 Aug; 2020 Jan 17. PMID: 31954708.
Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures.Melero R, Sorzano COS, Foster B, Vilas JL, Martínez M, Marabini R, Ramírez-Aportela E, Sanchez-Garcia R, Herreros D, Del Caño L, Losana P, Fonseca-Reyna YC, Conesa P, Wrapp D, Chacon P, McLellan JS, Tagare HD, Carazo JM. bioRxiv. 2020 Jul 8; 2020 Jul 8. PMID: 32676604.
Imaging of Injectable Hydrogels Delivered into Myocardium with SPECT/CT.Uman S, Wang LL, Thorn SL, Liu Z, Duncan JS, Sinusas AJ, Burdick JA. Adv Healthc Mater. 2020 Jul; 2020 Jun 15. PMID: 32543053.
A general-purpose Monte Carlo particle transport code based on inverse transform sampling for radiotherapy dose calculation.Liang Y, Muhammad W, Hart GR, Nartowt BJ, Chen ZJ, Yu JB, Roberts KB, Duncan JS, Deng J. Sci Rep. 2020 Jun 17; 2020 Jun 17. PMID: 32555530.
Sparse Data-Driven Learning for Effective and Efficient Biomedical Image Segmentation.Onofrey JA, Staib LH, Huang X, Zhang F, Papademetris X, Metaxas D, Rueckert D, Duncan JS. Annu Rev Biomed Eng. 2020 Jun 4; 2020 Mar 13. PMID: 32169002.
Extracellular pH mapping of liver cancer on a clinical 3T MRI scanner.Coman D, Peters DC, Walsh JJ, Savic LJ, Huber S, Sinusas AJ, Lin M, Chapiro J, Constable RT, Rothman DL, Duncan JS, Hyder F. Magn Reson Med. 2020 May; 2019 Nov 5. PMID: 31691371.
ESTIMATING REPRODUCIBLE FUNCTIONAL NETWORKS ASSOCIATED WITH TASK DYNAMICS USING UNSUPERVISED LSTMS.Dvornek NC, Ventola P, Duncan JS. Proc IEEE Int Symp Biomed Imaging. 2020 Apr; 2020 May 22. PMID: 34422224.
A SEMI-SUPERVISED JOINT LEARNING APPROACH TO LEFT VENTRICULAR SEGMENTATION AND MOTION TRACKING IN ECHOCARDIOGRAPHY.Ta K, Ahn SS, Lu A, Stendahl JC, Sinusas AJ, Duncan JS. Proc IEEE Int Symp Biomed Imaging. 2020 Apr; 2020 May 22. PMID: 33005289.
Graph Embedding Using Infomax for ASD Classification and Brain Functional Difference Detection.Li X, Dvornek NC, Zhuang J, Ventola P, Duncan J. Proc SPIE Int Soc Opt Eng. 2020 Feb; 2020 Feb 28. PMID: 33082616.
Unsupervised Motion Tracking of Left Ventricle in Echocardiography.Ahn SS, Ta K, Lu A, Stendahl JC, Sinusas AJ, Duncan JS. Proc SPIE Int Soc Opt Eng. 2020 Feb; 2020 Mar 16. PMID: 32994659.
Prostatic Artery Embolization in Nonindex Benign Prostatic Hyperplasia Patients: Single-center Outcomes for Urinary Retention and Gross Prostatic Hematuria.Ayyagari R, Powell T, Staib L, Chapiro J, Perez-Lozada JC, Bhatia S, Chai T, Schoenberger S, Devito R. Urology. 2020 Feb; 2019 Nov 14. PMID: 31734349.
Regional myocardial strain analysis via 2D speckle tracking echocardiography: validation with sonomicrometry and correlation with regional blood flow in the presence of graded coronary stenoses and dobutamine stress.Stendahl JC, Parajuli N, Lu A, Boutagy NE, Guerrera N, Alkhalil I, Lin BA, Staib LH, O'Donnell M, Duncan JS, Sinusas AJ. Cardiovasc Ultrasound. 2020 Jan 15; 2020 Jan 15. PMID: 31941514.
Molecular Imaging of Extracellular Tumor pH to Reveal Effects of Locoregional Therapy on Liver Cancer Microenvironment.Savic LJ, Schobert IT, Peters D, Walsh JJ, Laage-Gaupp FM, Hamm CA, Tritz N, Doemel LA, Lin M, Sinusas A, Schlachter T, Duncan JS, Hyder F, Coman D, Chapiro J. Clin Cancer Res. 2020 Jan 15; 2019 Oct 3. PMID: 31582517.
Measuring local-directional resolution and local anisotropy in cryo-EM maps.Vilas JL, Tagare HD, Vargas J, Carazo JM, Sorzano COS. Nat Commun. 2020 Jan 2; 2020 Jan 2. PMID: 31896756.
Efficient Shapley Explanation For Features Importance Estimation Under Uncertainty.Li X, Zhou Y, Dvornek NC, Gu Y, Ventola P, Duncan JS. Med Image Comput Comput Assist Interv. 2020; 2020 Sep 29. PMID: 34308439.
Demographic-Guided Attention in Recurrent Neural Networks for Modeling Neuropathophysiological Heterogeneity.Dvornek NC, Li X, Zhuang J, Ventola P, Duncan JS. Mach Learn Med Imaging. 2020; 2020 Sep 29. PMID: 34308438.
Adaptive Checkpoint Adjoint Method for Gradient Estimation in Neural ODE.Zhuang J, Dvornek N, Li X, Tatikonda S, Papademetris X, Duncan J. Proc Mach Learn Res. 2020. PMID: 34308361.
Prostatic Artery Embolization Using 100-300-μm Trisacryl Gelatin Microspheres to Treat Lower Urinary Tract Symptoms Attributable to Benign Prostatic Hyperplasia: A Single-Center Outcomes Analysis with Medium-Term Follow-up.Ayyagari R, Powell T, Staib L, Chapiro J, Raja A, Bhatia S, Chai T, Schoenberger S, Devito R. J Vasc Interv Radiol. 2020 Jan; 2019 Nov 23. PMID: 31771896.

2019

Domain-Agnostic Learning with Anatomy-Consistent Embedding for Cross-Modality Liver Segmentation.Yang J, Dvornek NC, Zhang F, Zhuang J, Chapiro J, Lin M, Duncan JS. IEEE Int Conf Comput Vis Workshops. 2019 Oct; 2020 Mar 5. PMID: 34676308.
Decision Explanation and Feature Importance for Invertible Networks.Zhuang J, Dvornek NC, Li X, Yang J, Duncan JS. IEEE Int Conf Comput Vis Workshops. 2019 Oct; 2020 Mar 5. PMID: 33024924.
Graph Neural Network for Interpreting Task-fMRI Biomarkers.Li X, Dvornek NC, Zhou Y, Zhuang J, Ventola P, Duncan JS. Med Image Comput Comput Assist Interv. 2019 Oct; 2019 Oct 10. PMID: 32984866.
Unsupervised Domain Adaptation via Disentangled Representations: Application to Cross-Modality Liver Segmentation.Yang J, Dvornek NC, Zhang F, Chapiro J, Lin M, Duncan JS. Med Image Comput Comput Assist Interv. 2019 Oct; 2019 Oct 10. PMID: 32377643.