A full list of publications is available at Google Scholar
| Year | Authors | Title | Journal/Book/Conference | Link |
|---|---|---|---|---|
| 2025 | JW Carrizales, MJ Flakus, D Fairbourn, W Shao, SE Gerard, JE Bayouth, GE Christensen, and JM Reinhardt | 4DCT image artifact detection using deep learning | Medical Physics | DOI |
| 2025 | DS Carmo, AA Pezzulo, RA Villacreses, ML Eisenbeisz, RL Anderson, SEV Dorin, L Rittner, RA Lotufo, SE Gerard et al. | Manual segmentation of opacities and consolidations on CT of long COVID patients from multiple annotators | Scientific Data | DOI |
| 2025 | S Erattakulangara, K Kelat, K Burnham, R Balbi, SE Gerard, D Meyer, and SG Lingala | Open-source manually annotated vocal tract database for automatic segmentation from 3D MRI using deep learning: Benchmarking 2D and 3D convolutional and transformer networks | Journal of Voice | DOI |
| 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 | DOI |
| 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 |