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JosephBrunetJosephBrunet
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‎assets/css/extended/custom.css‎

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.post-content li {
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margin-bottom: 1.5em !important;
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margin-bottom: 1em !important;
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}
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.pub-list li {
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list-style: none;
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position: relative;
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padding-left: 1.4rem; /* space between square and text */
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margin-bottom: 0.7rem;
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}
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.pub-list li::before {
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content: "";
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position: absolute;
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left: 0;
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top: 0.55rem; /* vertical alignment */
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width: 8px; /* square size */
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height: 8px;
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background: currentColor; /* your accent orange */
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border-radius: 2px; /* optional: slightly rounded */
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}
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/* Hover effect stays the same */
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.pub-list li:hover {
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background: rgba(0,0,0,0.05);
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transform: translateX(3px);
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transition: 0.2s ease;
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}
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‎content/publications/_index.md‎

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You can also find my scientific publications on <a href="https://scholar.google.com/citations?user=7T_yo4UAAAAJ" class="text-link">Google Scholar</a>
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<div class='pub-list'>
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---
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### 2026
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- VMW Michels, A Szmul, J Jacob, H Dejea, BS de Bakker, JAF Huirne, ..., et al., **Revealing the unseen: 3D synchrotron X-Ray imaging of uterine vasculature in adenomyosis**, _Angiogenesis_, 2026. <a href='https://doi.org/10.1007/s10456-025-10004-w' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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### 2025
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- E Newham, AL Parmenter, J Chen, C Disney, T Snow, **J Brunet**, et al., **Multimodal X-ray imaging reveals hierarchical fibre mechanics**, _BioRxiv preprint_, 2025. <a href='https://doi.org/10.1101/2025.09.19.677294' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- S Rahmani, DJ Jafree, PD Lee, P Tafforeau, **J Brunet**, et al., **Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography**, _npj Imaging_, 2025. <a href='https://doi.org/10.1038/s44303-025-00090-2' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- A Mirone, **J Brunet**, T Urban, et al., **Eikonal Phase Retrieval: unleashing the potential of fourth-generation sources for enhanced propagation-based tomography on biological samples**, _Synchrotron Radiation 32 (5), 2025_, 2025. <a href='https://doi.org/10.1364/opticaopen.26069182.v1' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- **J Brunet**, L Chestnutt, M Chourrout, et al., **Cardiotensor: A Python Library for Orientation Analysis and Tractography in 3D Cardiac Imaging**, _ArXiv preprint_, 2025
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- CL Walsh, **J Brunet**, D Stansby, et al., **The Human Organ Atlas**, _BioRxiv preprint_, 2025
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- Y Zhou, S Aslani, Y Javanmardi, **J Brunet**, et al., **Multiscale Segmentation using Hierarchical Phase-contrast Tomography and Deep Learning**, _BioRxiv preprint_, 2025. <a href='https://doi.org/10.1101/2025.05.15.654263' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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### 2024
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- Xian, R Patrick, **Brunet, Joseph**, Huang, Yuze, et al., A closer look at high-energy X-ray-induced bubble formation during soft tissue imaging, _Synchrotron Radiation_, 2024 **(Co-first author)**. <a href='https://doi.org/10.1107/s160057752400290x' class='text-link'><i class='fas fa-solid fa-file'></i> 10.1107/s160057752400290x</a>
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- SE Verleden, T Urban, **J Brunet**, et al., **Imaging Three-Dimensional Airway Morphology in Congenital Pulmonary Airway Malformation Using Hierarchical Phase-Contrast Tomography**, _American Journal of Respiratory and Critical Care Medicine_, 2024. <a href='https://doi.org/10.1164/rccm.202403-0509im' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- E Yagis, S Aslani, Y Jain, Y Zhou, S Rahmani, **J Brunet**, et al., **Deep learning for 3D vascular segmentation in hierarchical phase contrast tomography: a case study on kidney**, _Scientific Reports_, 2024. <a href='https://doi.org/10.1038/s41598-024-77582-5' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- **Brunet, Joseph**, Cook, Andrew C, Walsh, Claire L, et al., Multidimensional analysis of the adult human heart in health and disease using hierarchical phase-contrast tomography, _Radiology_, 2024 **(Cover of the July 2024 issue.)**. <a href='https://doi.org/10.1148/radiol.232731' class='text-link'><i class='fas fa-solid fa-file'></i> 10.1148/radiol.232731</a>
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- **J Brunet**, CL Walsh, P Tafforeau, et al., **Hierarchical phase-contrast tomography: a non-destructive multiscale imaging approach for whole human organs**, _Developments in X-Ray Tomography XV_, 2024. <a href='https://doi.org/10.1117/12.3028717' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- Verleden, Stijn E, Urban, Theresa, **Brunet, Joseph**, et al., Imaging Three-Dimensional Airway Morphology in Congenital Pulmonary Airway Malformation Using Hierarchical Phase-Contrast Tomography, _American Journal of Respiratory and Critical Care Medicine_, 2024. <a href='https://doi.org/10.1164/rccm.202403-0509IM' class='text-link'><i class='fas fa-solid fa-file'></i> 10.1164/rccm.202403-0509IM</a>
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- Y Jain, CL Walsh, E Yagis, S Aslani, S Nandanwar, Y Zhou, J Ha, ..., et al., **Vasculature segmentation in 3D hierarchical phase-contrast tomography images of human kidneys**, _BioRxiv preprint_, 2024. <a href='https://doi.org/10.1101/2024.08.25.609595' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- Jain, Yashvardhan, Walsh, Claire L, Yagis, Ekin, Aslani, Shahab, Nandanwar, Sonal, Zhou, Yang, Ha, Juhyung, Gustilo, Katherine S, **Brunet, Joseph**, et al., Vasculature segmentation in 3D hierarchical phase-contrast tomography images of human kidneys, _bioRxiv_, 2024. <a href='https://doi.org/10.1101/2024.08.25.609595' class='text-link'><i class='fas fa-solid fa-file'></i> 10.1101/2024.08.25.609595</a>
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- **J Brunet**, AC Cook, CL Walsh, et al., **Multidimensional analysis of the adult human heart in health and disease using hierarchical phase-contrast tomography**, _Radiology 312 (1), e232731, 2024_, 2024. <a href='https://doi.org/10.1101/2023.10.09.561474' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- **Brunet, Joseph**, Walsh, Claire, Tafforeau, Paul, et al., Hierarchical phase-contrast tomography: a non-destructive multiscale imaging approach for whole human organs, _Developments in X-Ray Tomography XV_, 2024. <a href='https://doi.org/doi.org/10.1117/12.3028717' class='text-link'><i class='fas fa-solid fa-file'></i> doi.org/10.1117/12.3028717</a>
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- S Rahmani, DJ Jafree, PD Lee, P Tafforeau, **J Brunet**, et al., **Mapping the blood vasculature in an intact human kidney using hierarchical phase-contrast tomography**, _BioRxiv preprint_, 2024. <a href='https://doi.org/10.1101/2023.03.28.534566' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- Yagis, Ekin, Aslani, Shahab, Jain, Yashvardhan, Zhou, Yang, Rahmani, Shahrokh, **Brunet, Joseph**, et al., Deep learning for 3D vascular segmentation in hierarchical phase contrast tomography: a case study on kidney, _Scientific Reports_, 2024. <a href='https://doi.org/10.1038/s41598-024-77582-5' class='text-link'><i class='fas fa-solid fa-file'></i> 10.1038/s41598-024-77582-5</a>
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- RP Xian, **J Brunet**, Y Huang, et al., **A closer look at high-energy X-ray-induced bubble formation during soft tissue imaging**, _Synchrotron Radiation 31 (3), 566-577, 2024_, 2024. <a href='https://doi.org/10.1101/2023.02.14.528474' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- Rahmani, Shahrokh, Jafree, Daniyal J, Lee, Peter D, Tafforeau, Paul, **Brunet, Joseph**, et al., Mapping the blood vasculature in an intact human kidney using hierarchical phase-contrast tomography, _bioRxiv_, 2024. <a href='https://doi.org/10.1101/2023.03.28.534566' class='text-link'><i class='fas fa-solid fa-file'></i> 10.1101/2023.03.28.534566</a>
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### 2023
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- **Brunet, J**, Pierrat, Baptiste, Adrien, J, et al., In situ visualization of aortic dissection propagation in notched rabbit aorta using synchrotron X-ray tomography, _Acta Biomaterialia_, 2023. <a href='https://doi.org/10.1016/j.actbio.2022.10.060' class='text-link'><i class='fas fa-solid fa-file'></i> 10.1016/j.actbio.2022.10.060</a>
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- A Mirone, **J Brunet**, L Admans, et al., **Eikonal phase retrieval: Unleashing the fourth generation sources potential for enhanced propagation based tomography on biological samples**, _ArXiv preprint_, 2023
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- E Yagis, S Aslani, Y Jain, Y Zhou, S Rahmani, **J Brunet**, et al., **Deep Learning for Vascular Segmentation and Applications in Phase Contrast Tomography Imaging**, _ArXiv preprint_, 2023
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- **J Brunet**, CL Walsh, WL Wagner, et al., **Preparation of large biological samples for high-resolution, hierarchical, synchrotron phase-contrast tomography with multimodal imaging compatibility**, _Nature Protocols_, 2023. <a href='https://doi.org/10.1038/s41596-023-00804-z' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- S Rahmani, DJ Jafree, PD Lee, P Tfforeau, J Jacob, A Bellier, ..., et al., **Micro to macro scale analysis of the intact human renal arterial tree with Synchrotron Tomography**, _BioRxiv preprint_, 2023. <a href='https://doi.org/10.1101/2024.08.06.605570' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- M Ackermann, P Tafforeau, **J Brunet**, et al., **Reply to: Intrapulmonary Shunt and Alveolar Dead Space in a Cohort of Patients with Acute COVID-19 Pneumonitis and Early Recovery**, _European Respiratory Journal_, 2023. <a href='https://doi.org/10.1183/13993003.02287-2022' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- **J Brunet**, B Pierrat, J Adrien, et al., **In situ visualization of aortic dissection propagation in notched rabbit aorta using synchrotron X-ray tomography**, _Acta Biomaterialia_, 2023. <a href='https://doi.org/10.1016/j.actbio.2022.10.060' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- **Brunet, J**, Walsh, CL, Wagner, WL, et al., Preparation of large biological samples for high-resolution, hierarchical, synchrotron phase-contrast tomography with multimodal imaging compatibility, _Nature protocols_, 2023. <a href='https://doi.org/10.1038/s41596-023-00804-z' class='text-link'><i class='fas fa-solid fa-file'></i> 10.1038/s41596-023-00804-z</a>
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- Ackermann, Maximilian, Tafforeau, Paul, **Brunet, Joseph**, et al., Comment on: Intrapulmonary shunt and alveolar dead space in a cohort of patients with acute COVID-19 pneumonitis and early recovery, _The European Respiratory Journal_, 2023. <a href='https://doi.org/10.1183/13993003.02121-2022' class='text-link'><i class='fas fa-solid fa-file'></i> 10.1183/13993003.02121-2022</a>
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### 2022
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- Mirone, Alessandro, **Brunet, Joseph**, Admans, Leandre, et al., Eikonal phase retrieval: Unleashing the fourth generation sources potential for enhanced propagation based tomography on biological samples, _arXiv preprint arXiv:2311.14745_, 2023. <a href='https://doi.org/10.48550/ARXIV.2311.14745' class='text-link'><i class='fas fa-solid fa-file'></i> 10.48550/ARXIV.2311.14745</a>
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- **J Brunet**, CL Walsh, WL Wagner, et al., **Preparation of large biological samples for high-resolution, hierarchical, multi-modal imaging**, _BioRxiv preprint_, 2022. <a href='https://doi.org/10.1101/2022.07.02.498430' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- Rahmani, Shahrokh, Jafree, Daniyal J, Lee, Peter D, Tfforeau, Paul, Jacob, Joseph, Bellier, Alexandre, Ackermann, Maximilian, Jonigk, Danny D, Shipley, Rebecca J, Long, David A, others, et al., Micro to macro scale analysis of the intact human renal arterial tree with Synchrotron Tomography, _BioRxiv_, 2023. <a href='https://doi.org/10.1101/2023.03.28.534566' class='text-link'><i class='fas fa-solid fa-file'></i> 10.1101/2023.03.28.534566</a>
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### 2021
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- **Brunet, J**, Pierrat, B, Adrien, Jérôme, et al., A novel method for in vitro 3D imaging of dissecting pressurized arterial segments using X-ray microtomography, _Experimental Mechanics_, 2021. <a href='https://doi.org/10.1007/s11340-020-00645-x' class='text-link'><i class='fas fa-solid fa-file'></i> 10.1007/s11340-020-00645-x</a>
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- **J Brunet**, et al., **Comprendre les mécanismes de dissection aortique: modélisation éléments finis et expérimentation in situ sous tomographie RX**, _Revue Européenne des Éléments Finis_, 2021. <a href='https://doi.org/10.1080/12506559.2001.9737566' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- **J Brunet**, et al., **Understanding the mechanisms of aortic dissection: finite element modeling and in situ experimentation with X-ray tomography**, _JTCVS Techniques_, 2021. <a href='https://doi.org/10.1016/j.xjtc.2020.10.006' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- **J Brunet**, B Pierrat, P Badel, et al., **A parametric study on factors influencing the onset and propagation of aortic dissection using the extended finite element method**, _IEEE Transactions on Biomedical Engineering_, 2021. <a href='https://doi.org/10.1109/tbme.2021.3056022' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- **Brunet, Joseph**, Pierrat, Baptiste, Badel, Pierre, et al., A parametric study on factors influencing the onset and propagation of aortic dissection using the extended finite element method, _IEEE Transactions on Biomedical Engineering_, 2021. <a href='https://doi.org/10.1109/TBME.2021.3056022' class='text-link'><i class='fas fa-solid fa-file'></i> 10.1109/TBME.2021.3056022</a>
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- **J Brunet**, B Pierrat, J Adrien, et al., **A novel method for in vitro 3D imaging of dissecting pressurized arterial segments using X-ray microtomography**, _Experimental Mechanics_, 2021. <a href='https://doi.org/10.1007/s11340-020-00645-x' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- **Brunet, Joseph**, et al., Understanding the mechanisms of aortic dissection: finite element modeling and in situ experimentation with X-ray tomography, _Thesis_, 2021
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- QH Abbasi, K Ahi, K AL-Dulaimi, A Al-Fuqaha, A Al-Sabaawi, ..., et al., **2021 Index IEEE Reviews in Biomedical Engineering Vol. 14**, _IEEE Reviews in Biomedical Engineering_, 2021. <a href='https://doi.org/10.1109/rbme.2021.3061839' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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### 2020
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- **Brunet, Joseph**, Pierrat, Baptiste, Badel, Pierre, et al., Review of current advances in the mechanical description and quantification of aortic dissection mechanisms, _IEEE Reviews in Biomedical Engineering_, 2020. <a href='https://doi.org/10.1109/RBME.2019.2950140' class='text-link'><i class='fas fa-solid fa-file'></i> 10.1109/RBME.2019.2950140</a>
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- **J Brunet**, B Pierrat, P Badel, et al., **Review of current advances in the mechanical description and quantification of aortic dissection mechanisms**, _IEEE Reviews in Biomedical Engineering_, 2020. <a href='https://doi.org/10.1109/rbme.2019.2950140' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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### 2019
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- **Brunet, J**, Pierrat, B, Maire, E, et al., A combined experimental-numerical lamellar-scale approach of tensile rupture in arterial medial tissue using X-ray tomography, _Journal of the mechanical behavior of biomedical materials_, 2019. <a href='https://doi.org/10.1016/j.jmbbm.2019.03.028' class='text-link'><i class='fas fa-solid fa-file'></i> 10.1016/j.jmbbm.2019.03.028</a>
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- **J Brunet**, B Pierrat, E Maire, et al., **A combined experimental-numerical lamellar-scale approach of tensile rupture in arterial medial tissue using X-ray tomography**, _Journal of the Mechanical Behavior of Biomedical Materials_, 2019. <a href='https://doi.org/10.1016/j.jmbbm.2019.03.028' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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- **Brunet, J**, Pierrat, B, Badel, P, et al., A numerical design of experiment approach to understand aortic dissection onset and propagation, _Computer Methods in Biomechanics and Biomedical Engineering_, 2019. <a href='https://doi.org/10.1080/10255842.2020.1713458' class='text-link'><i class='fas fa-solid fa-file'></i> 10.1080/10255842.2020.1713458</a>
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- **J Brunet**, B Pierrat, P Badel, et al., **A numerical design of experiment approach to understand aortic dissection onset and propagation**, _Computer Methods in Biomechanics and Biomedical Engineering_, 2019. <a href='https://doi.org/10.1080/10255842.2020.1713458' class='text-link'><i class='fas fa-solid fa-file'></i></a>
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