Publications

A full list of publications is available at Google Scholar

Year	Authors	Title	Journal/Book/Conference	Link
2024	MFA Chaudhary, SS Hosseini, RG Barr, JM Reinhardt, EA Hoffman, and SE Gerard	Bridging the task barriers: Online knowledge distillation across tasks for semi-supervised mediastinal segmentation in CT	Machine Learning in Medical Imaging	DOI
2024	MFA Chaudhary, SE Gerard, GE Christensen, CB Cooper, JD Schroeder, EA Hoffman, and JM Reinhardt	LungViT: Ensembling Cascade of Texture Sensitive Hierarchical Vision Transformers for Cross-Volume Chest CT Image-to-Image Translation	IEEE Transactions on Medical Imaging	DOI
2024	AI Ritchie, GC Donaldson, EA Hoffman, JP Allinson, CI Bloom, CE Bolton, G Choudhury, SE Gerard, J Guo et al.	Structural predictors of lung function decline in young smokers with normal spirometry	American Journal of Respiratory and Critical Care Medicine	DOI
2024	SE Gerard, TM Dougherty, P Nagpal, D Jin, MK Han, JD Newell Jr., PK Saha, AP Comellas, CB Cooper et al.	Vessel and airway characteristics in one-year CT-defined rapid emphysema progression: SPIROMICS	Annals of the American Thoracic Society	DOI
2023	ZW Althof, SE Gerard, A Eskandari, MS Galizia, EA Hoffman, and JM Reinhardt	Attention U-net for automated pulmonary fissure integrity analysis in lung computed tomography images	Scientific Reports	DOI
2023	SE Gerard, MFA Chaudhary, J Herrmann, GE Christensen, R San Jose Estepar, JM Reinhardt, and EA Hoffman	Direct estimation of regional lung volume change from paired and single CT images using residual regression neural network	Medical Physics	DOI
2023	KT Martin, Y Xin, TG Gaulton, M Victor, RR Santiago, T Kim, CCA Morais, AA Kazimi, M Connell et al.	Electrical impedance tomography identifies evolution of regional perfusion in a porcine model of acute respiratory distress syndrome	Anesthesiology	DOI
2023	Y Xin, T Kim, T Winkler, G Brix, T Gaulton, SE Gerard, J Herrmann, KT Martin, M Victor et al.	Improving pulmonary perfusion assessment by dynamic contrast-enhanced computed tomography in an experimental lung injury model	Journal of Applied Physiology	DOI
2023	MFA Chaudhary, EA Hoffman, J Guo, AP Comellas, JD Newell, P Nagpal, S Fortis, GE Christensen, SE Gerard et al.	Predicting severe chronic obstructive pulmonary disease exacerbations using quantitative CT: A retrospective model development and external validation study	The Lancet Digital Health	DOI
2023	EM Wallat, AE Wuschner, MJ Flakus, SE Gerard, GE Christensen, JM Reinhardt, and JE Bayouth	Predicting pulmonary ventilation damage after radiation therapy for non-small cell lung cancer using a ResNet generative adversarial network	Medical Physics	DOI
2023	PL Silva, FF Cruz, CM Martins, J Herrmann, SE Gerard, Y Xin, M Cereda, L Ball, P Pelosi et al.	A specific combination of laboratory data is associated with overweight lungs in patients with COVID-19 pneumonia at hospital admission: Secondary cross-sectional analysis of a randomized clinical trial	Frontiers in Medicine	DOI
2022	AE Wuschner, MJ Flakus, EM Wallat, JM Reinhardt, D Shanmuganayagam, GE Christensen, SE Gerard, and JE Bayouth	CT-derived vessel segmentation for analysis of post-radiation therapy changes in vasculature and perfusion	Frontiers in Physiology	DOI
2022	L Ball, C Robba, J Herrmann, SE Gerard, Y Xin, M Pigati, A Berardino, F Iannuzzi, D Battaglini et al.	Early versus late intubation in COVID-19 patients failing helmet CPAP: A quantitative computed tomography study	Respiratory Physiology & Neurobiology	DOI
2022	Z Yuan, J Herrmann, S Murthy, K Peters, SE Gerard, HT Nia, KR Lutchen, and B Suki	A personalized spring network representation of emphysematous lungs from CT images	Frontiers in Network Physiology	DOI
2022	EA Hermann, A Motahari, EA Hoffman, N Allen, AG Bertoni, DA Bluemke, A Eskandari, SE Gerard, J Guo et al.	Pulmonary blood volume among older adults in the community: The MESA lung study	Circulation: Cardiovascular Imaging	DOI
2022	E Hermann, A Motahari, E Hoffman, N Allen, E Angelini, A Bertoni, D Bluemke, A Eskandari, S Gerard et al.	Quantitative CT emphysema subtypes and pulmonary blood volume on dual-energy CT: The MESA Lung Study	06.03 - Tobacco, smoking control and health education	DOI
2022	Y Pan, D Wang, MFA Chaudhary, W Shao, SE Gerard, OC Durumeric, SP Bhatt, RG Barr, EA Hoffman et al.	Robust measures of image-registration-derived lung biomechanics in SPIROMICS	Journal of Imaging	DOI
2022	MFA Chaudhary, SE Gerard, D Wang, GE Christensen, CB Cooper, JD Schroeder, EA Hoffman, and JM Reinhardt	Single volume lung biomechanics from chest computed tomography using a mode preserving generative adversarial network	2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI)	DOI
2022	M Connell, Y Xin, SE Gerard, J Herrmann, PK Shah, KT Martin, E Rezoagli, D Ippolito, J Rajaei et al.	Unsupervised segmentation and auantification of COVID-19 lesions on computed tomography scans using CycleGAN	Methods	DOI
2021	P Nagpal, A Motahari, SE Gerard, J Guo, JM Reinhardt, AP Comellas, EA Hoffman, and DW Kaczka	Case studies in physiology: Temporal variations of the lung parenchyma and vasculature in asymptomatic COVID-19 pneumonia: A multispectral CT assessment	Journal of Applied Physiology	DOI
2021	P Delvecchio, Y Xin, K Martin, S Gerard, H Hamedani, J Herrmann, S Humayun, A Lenart, U Sidhu et al.	A clinically relevant and reliable model for preclinical research of ARDS syndrome	American Thoracic Society	DOI
2021	L Ball, C Robba, L Maiello, J Herrmann, SE Gerard, Y Xin, D Battaglini, I Brunetti, G Minetti et al.	Computed tomography assessment of PEEP-induced alveolar recruitment in patients with severe COVID-19 pneumonia	Critical Care	DOI
2021	M Chaudhary, E Hoffman, A Comellas, J Guo, S Fortis, S Bodduluri, F Abtin, R Barr, S Bhatt et al.	CT texture features predict severe COPD exacerbations in SPIROMICS	American Thoracic Society	DOI
2021	SE Gerard, J Herrmann, Y Xin, KT Martin, E Rezoagli, D Ippolito, G Bellani, M Cereda, J Guo et al.	CT image segmentation for inflamed and fibrotic lungs using a multi-resolution convolutional neural network	Scientific Reports	DOI
2021	K Martin, Y Xin, J Herrmann, S Gerard, P Delvecchio, S Humayun, A Lenart, U Sidhu, N Abate et al.	Diminished redistribution of aeration and perfusion with prone ventilation in late stage experimental lung injury	American Thoracic Society	DOI
2021	Y Xin, K Martin, CCA Morais, P Delvecchio, SE Gerard, H Hamedani, J Herrmann, N Abate, A Lenart et al.	Diminishing efficacy of prone positioning with late application in evolving lung injury	Critical Care Medicine	DOI
2021	J Herrmann, SE Gerard, W Shao, Y Xin, M Cereda, JM Reinhardt, GE Christensen, EA Hoffman, and DW Kaczka	Effects of lung injury on regional aeration and expiratory time constants: Insights from four-dimensional computed tomography image registration	Frontiers in Physiology	DOI
2021	D Battaglini, S Caiffa, G Gasti, E Ciaravolo, C Robba, J Herrmann, SE Gerard, M Bassetti, P Pelosi et al.	An experimental pre-post study on the efficacy of respiratory physiotherapy in severe critically iII COVID-19 patients	Journal of Clinical Medicine	DOI
2021	Y Xin, A Lenart, K Martin, P Delvecchio, S Gerard, H Hamedani, J Herrmann, S Humayun, U Sidhu et al.	High-resolution responses to prone positioning and PEEP therapy in a large animal model of evolving lung injury	American Thoracic Society	DOI
2021	L Ball, C Robba, J Herrmann, SE Gerard, Y Xin, M Mandelli, D Battaglini, I Brunetti, G Minetti et al.	Lung distribution of gas and blood volume in critically ill COVID-19 patients: A quantitative dual-energy computed tomography study	Critical Care	DOI
2021	Y Xin, J Herrmann, S Gerard, P Delvecchio, K Martin, R Rizi, D Kaczka, and M Cereda	Non-linear inflation dynamics increase during progression of experimental lung injury	American Thoracic Society	DOI
2021	Y Xin, J Herrmann, K Martin, S Gerard, P Delvecchio, S Humayun, A Lenart, U Sidhu, M Petrov et al.	Prone ventilation in lung injury: The declining benefits of vertical axis ventilation and perfusion matching at late stages of injury	American Thoracic Society	DOI
2021	E Hermann, G Hiura, E Hoffman, A Motahari, S Gerard, P Nagpal, A Eskandari, J Go, N Allen et al.	Pulmonary blood volume in older adults assessed by dual-energy computed tomography: The multi-ethnic study of atherosclerosis (MESA) lung study	American Thoracic Society	DOI
2021	A Eskandari, P Nagpal, J Guo, A Motahari, S Gerard, D Kaczka, E Hermann, G Hiura, B Smith et al.	Quality control for quantitation of regional pulmonary perfused blood volume via dual-energy CT scanning in a large multi-center cohort: The MESA lung study	American Thoracic Society	DOI
2021	X He, J Guo, X Zhang, H Bi, S Gerard, D Kaczka, A Motahari, E Hoffman, J Reinhardt et al.	Recursive refinement network for deformable lung registration between exhale and inhale CT scans		DOI
2021	J Herrmann, SE Gerard, JM Reinhardt, EA Hoffman, and DW Kaczka	Regional gas transport during conventional and oscillatory ventilation assessed by xenon-enhanced computed tomography	Annals of Biomedical Engineering	DOI
2021	MFA Chaudhary, SE Gerard, D Wang, GE Christensen, CB Cooper, JD Schroeder, EA Hoffman, and JM Reinhardt	Single volume lung biomechanics from chest computed tomography using a mode preserving generative adversarial network		DOI
2021	P Silva, F Cruz, L Ball, J Herrmann, S Gerard, Y Xin, P Pelosi, and P Rocco	Time course of chest computed tomography findings and biomarkers in COVID-19 pneumonia patients	American Thoracic Society	DOI
2021	M Connell, Y Xin, S Gerard, J Herrmann, P Shah, K Martin, E Rezoagli, D Ippolito, J Rajaei et al.	Unsupervised segmentation and quantification of COVID-19 lesions on computed tomography scans using CycleGAN	American Thoracic Society	DOI
2020	Y Pan, GE Christensen, OC Durumeric, SE Gerard, SP Bhatt, RG Barr, EA Hoffman, and JM Reinhardt	Assessment of lung biomechanics in COPD using image registration	2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI)	DOI
2020	ZW Althof, SE Gerard, Y Pan, GE Christensen, EA Hoffman, and JM Reinhardt	Automatic quantification of pulmonary fissure integrity: A repeatability analysis	2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI)	DOI
2020	S Gerard, J Reinhardt, G Christensen, G Washko, and R San Jose Estepar	Clinical associations of direct estimation of local tissue expansion in smokers using deep learning	American Thoracic Society	DOI
2020	SE Gerard, JM Reinhardt, GE Christensen, and RSJ Estepar	Estimating local tissue expansion in thoracic computed tomography images using convolutional neural networks	2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI)	DOI
2020	J Herrmann, S Gerard, W Shao, Y Xin, M Cereda, J Reinhardt, G Christensen, E Hoffman, and D Kaczka	Expiratory de-aeration occurs faster in poorly- vs. normally-aerated regions of the injured lung	American Thoracic Society	DOI
2020	SE Gerard, J Herrmann, DW Kaczka, G Musch, A Fernandez-Bustamante, and JM Reinhardt	Multi-resolution convolutional neural networks for fully automated segmentation of acutely injured lungs in multiple species	Medical Image Analysis	DOI
2020	W Shao, TJ Patton, SE Gerard, Y Pan, JM Reinhardt, OC Durumeric, JE Bayouth, and GE Christensen	N-phase local expansion ratio for characterizing out-of-phase lung ventilation	IEEE transactions on medical imaging	DOI
2020	JC Ross, P Nardelli, J Onieva, SE Gerard, R Harmouche, Y Okajima, AA Diaz, G Washko, and R San Jose Estepar	An open-source framework for pulmonary fissure completeness assessment	Computerized Medical Imaging and Graphics: The Official Journal of the Computerized Medical Imaging Society	DOI
2020	J Herrmann, SE Gerard, W Shao, ML Hawley, JM Reinhardt, GE Christensen, EA Hoffman, and DW Kaczka	Quantifying regional lung deformation using four-dimensional computed tomography: A comparison of conventional and oscillatory ventilation	Frontiers in Physiology	DOI
2019	SE Gerard, TJ Patton, GE Christensen, JE Bayouth, and JM Reinhardt	FissureNet: A deep learning approach for pulmonary fissure detection in CT images	IEEE transactions on medical imaging	DOI
2019	M Flakus, A Wuschner, E Wallat, W Shao, S Gerard, G Christensen, J Reinhardt, and J Bayouth	Improving the accuracy of 4DCT-based ventilation measurements using multiple phases	Medical Physics	DOI
2019	J Bayouth, E Wallat, A Wuschner, M Flakus, T Patton, W Shao, S Gerard, J Reinhardt, G Christensen et al.	Longitudinal changes in lung tissue elasticity following radiation therapy	Medical Physics
2019	J Herrmann, S Gerard, W Shao, J Reinhardt, G Christensen, E Hoffman, M Hawley, and D Kaczka	Multi-frequency oscillatory ventilation minimizes spatial gradients of regional strain using 4D CT image registration in porcine lung injury	American Thoracic Society	DOI
2019	S Bodduluri, A Nakhmani, P Kandhare, T Patel, S Gerard, J Reinhardt, C Wilson, N Bhakta, P Castaldi et al.	Prediction of emphysema and airway disease from spirometry using neural networks	American Thoracic Society	DOI
2019	SE Gerard, and JM Reinhardt	Pulmonary lobe segmentation using a sequence of convolutional neural networks for marginal learning	2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019)	DOI
2019	E Wallat, M Flakus, A Wuschner, W Shao, S Gerard, T Patton, G Christensen, J Reinhardt, A Baschnagel et al.	Radiation dose response model for ventilation change using all phases of 4DCT	Medical Physics
2019	J Kipritidis, BA Tahir, G Cazoulat, MS Hofman, S Siva, J Callahan, N Hardcastle, T Yamamoto, GE Christensen et al.	The VAMPIRE challenge: A multi-institutional validation study of CT ventilation imaging	Medical Physics	DOI
2019	A Wuschner, E Wallat, M Flakus, S Gerard, T Patton, J Reinhardt, G Christensen, and J Bayouth	Vasculature anatomy change in nonsmall cell lung cancer patients post radiation therapy	Medical Physics
2018	S Bodduluri, ASK Puliyakote, SE Gerard, JM Reinhardt, EA Hoffman, JD Newell, HP Nath, MK Han, GR Washko et al.	Airway fractal dimension predicts respiratory morbidity and mortality in COPD	The Journal of Clinical Investigation	DOI
2018	W Shao, TJ Patton, SE Gerard, Y Pan, JM Reinhardt, JE Bayouth, OC Durumeric, and GE Christensen	Detecting out-of-phase ventilation using 4DCT to improve radiation therapy for lung cancer	Image Analysis for Moving Organ, Breast, and Thoracic Images	DOI
2018	TJ Patton, SE Gerard, W Shao, GE Christensen, JM Reinhardt, AM Baschnagell, and JE Bayouth	Longitudinal assessment of 4DCT-derived ventilation change following radiation therapy	Medical Physics
2018	TJ Patton, SE Gerard, W Shao, GE Christensen, JM Reinhardt, and JE Bayouth	Quantifying ventilation change due to radiation therapy using 4DCT Jacobian calculations	Medical Physics	DOI
2018	W Shao, SE Gerard, Y Pan, TJ Patton, JM Reinhardt, OC Durumeric, JE Bayouth, and GE Christensen	Sensitivity analysis of Jacobian determinant used in treatment planning for lung cancer	Medical Imaging 2018: Image Processing	DOI
2018	J Bayouth, T Patton, S Gerard, W Shao, G Christensen, J Reinhardt, and A Baschnagel	Signal processing analysis of breathing rates show improved spectral coherence when human subjects receive musical melody and voice instruction guidance	Medical Physics
2018	S Bodduluri, S Gerard, J Reinhardt, E Hoffman, J Newell, H Nath, M Dransfield, and S Bhatt	Silent zones of lung disease in active smokers	American Thoracic Society
2018	SE Gerard, J Herrmann, DW Kaczka, and JM Reinhardt	Transfer learning for segmentation of injured lungs using coarse-to-fine convolutional neural networks	Image Analysis for Moving Organ, Breast, and Thoracic Images	DOI
2017	J Bayouth, T Patton, S Gerard, G Christensen, A Baschnagel, and J Reinhardt	Clinical application of a lung function planning technique designed to improve toxicity	Medical Physics
2017	J Bayouth, T Patton, S Gerard, G Christensen, A Baschnagel, and J Reinhardt	Reducing patient respiration induced 4DCT image artifacts	Medical Physics
2017	T Patton, S Gerard, G Christensen, J Reinhardt, and J Bayouth	Removing interpolation artifacts in respiratory-gated 4DCT for improved ventilation estimation	Medical Physics
2017	J Kipritidis, G Cazoulat, B Tahir, M Hofman, S Siva, J Callahan, T Yamamoto, G Christensen, J Reinhardt et al.	The VAMPIRE challenge: Results of an international multi-institutional validation study to evaluate CT ventilation imaging algorithms	Medical Physics
2016	SE Gerard, HJ Johnson, JE Bayouth, GE Christensen, K Du, J Guo, and JM Reinhardt	Alpha shapes for lung segmentation in the presence of large tumors	6th International Workshop on Pulmonary Image Analysis
2016	Y Pan, GE Christensen, OC Durumeric, SE Gerard, JM Reinhardt, and GD Hugo	Current-and varifold-based registration of lung vessel and airway trees	2016 IEEE Conference on Computer Vision and Pattern Recognition Workshops (CVPRW)	DOI
2016	B Zhao, GE Christensen, JH Song, Y Pan, SE Gerard, JM Reinhardt, K Du, T Patton, JM Bayouth et al.	Tissue-volume preserving deformable image registration for 4DCT pulmonary images	2016 IEEE Conference on Computer Vision and Pattern Recognition Workshops (CVPRW)	DOI
2015	SE Gerard, GE Christensen, JE Bayouth, S Bodduluri, Y Pan, J Guo, K Du, JH Song, B Zhao et al.	4D lung CT segmentation for radiation therapy applications	ICART: Imaging and Computer Assistance in Radiation Therapy
2015	AM Nuotio-Antar, N Poungvarin, M Li, M Schupp, M Mohammad, S Gerard, F Zou, and L Chan	FABP4-Cre Mediated Expression of constitutively active ChREBP protects against obesity, fatty liver, and insulin resistance	Endocrinology	DOI
2015	K Du, T Patton, J Reinhardt, G Christensen, B Zhao, S Gerard, Y Pan, and J Bayouth	Lobar-level lung ventilation analysis using 4DCT and deformable image registration	Medical Physics	DOI