Publications

A full list of publications is available at Google Scholar

Year	Authors	Title	Journal/Book/Conference	Link
2024	S Fortis, J Guo, P Nagpal, MFA Chaudhary, JD Newell Jr., SE Gerard, MK Han, EA Kazerooni, FJ Martinez et al.	Association of ground glass opacities with systemic inflammation and progression of emphysema	American Journal of Respiratory and Critical Care Medicine	DOI
2024	EA Hermann, A Motahari, EA Hoffman, Y Sun, N Allen, ED Angelini, AG Bertoni, DA Bluemke, SE Gerard et al.	Associations of pulmonary microvascular blood volume with percent emphysema and CT emphysema subtypes in the community: The MESA Lung study	Thorax	DOI
2024	MFA Chaudhary, JM Reinhardt, and SE Gerard	Beyond intensity transforms: Medical image synthesis under large deformation	Simulation and Synthesis in Medical Imaging
2024	DS Carmo, AA Pezzulo, RA Villacreses, ML Eisenbeisz, RL Anderson, SEV Dorin, L Rittner, RA Lotufo, SE Gerard et al.	Long COVID Iowa-UNICAMP		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	D Lagier, C Zeng, DW Kaczka, M Zhu, K Grogg, SE Gerard, JM Reinhardt, GCM Ribeiro, A Rashid et al.	Mechanical ventilation guided by driving pressure optimizes local pulmonary biomechanics in an ovine model	Science Translational Medicine	DOI
2024	DS Carmo, JA Ribeiro, AP Comellas, JM Reinhardt, SE Gerard, L Rittner, and RA Lotufo	MEDPSeg: Hierarchical polymorphic multitask learning for the segmentation of ground-glass opacities, consolidation, and pulmonary structures on computed tomography		DOI
2024	K Kelat, SE Gerard, and C Mello-Thoms	Modeling decision making in breast cancer screening using deep learning: Usability of a Gabor convolutional layer	Medical Imaging 2024: Image Perception, Observer Performance, and Technology Assessment	DOI
2024	E Rezoagli, Y Xin, D Signori, W Sun, S Gerard, KL Delucchi, A Magliocca, G Vitale, M Giacomini et al.	Phenotyping COVID-19 respiratory failure in spontaneously breathing patients with AI on lung CT-scan	Critical Care	DOI
2024	S Spina, L Mantz, Y Xin, DC Moscho, R Ribeiro De Santis Santiago, L Grassi, A Nova, SE Gerard, EA Bittner et al.	The pleural gradient does not reflect the superimposed pressure in patients with class III obesity	Critical Care	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, PK Saha, AP Comellas, CB Cooper et al.	Vessel and airway characteristics in one-year computed tomography--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	DS Carmo, RA Tudas, AP Comellas, L Rittner, RA Lotufo, JM Reinhardt, and SE Gerard	Automatic segmentation of lung findings in CT and application to Long COVID		DOI
2023	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
2023	SE Gerard, MFA Chaudhary, J Herrmann, GE Christensen, RSJ 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, 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		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 nonsmall 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 Multi-Ethnic Study of Atherosclerosis (MESA) lung study	Circulation. Cardiovascular imaging	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 quantification of COVID-19 lesions on computed Tomography scans using CycleGAN	Methods (San Diego, Calif.)	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	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	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	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		DOI
2021	Y Xin, K Martin, CC 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	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	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
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	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	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 RS 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	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	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
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, 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	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
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