Reyes, Mauricio

Mahapatra, Dwarikanath; Tennakoon, Ruwan; George, Yasmeen; Roy, Sudipta; Bozorgtabar, Behzad; Ge, Zongyuan; Reyes, Mauricio (2024). ALFREDO: Active Learning with FeatuRe disEntangelement and DOmain adaptation for medical image classification. Medical image analysis, 97(103261), p. 103261. Elsevier 10.1016/j.media.2024.103261

Pahud de Mortanges, Aurélie; Luo, Haozhe; Shu, Shelley Zixin; Kamath, Amith; Suter, Yannick; Shelan, Mohamed; Pöllinger, Alexander; Reyes, Mauricio (2024). Orchestrating explainable artificial intelligence for multimodal and longitudinal data in medical imaging. NPJ digital medicine, 7(1) Nature Publishing Group 10.1038/s41746-024-01190-w

Poel, Robert; Rüfenacht, Elias; Fix, Michael; Scheib, Stefan; Reyes, Mauricio; Ermis, Ekin (May 2024). Clinical evaluation of a deep learning based auto-segmentation model for intracranial organs at risk. Radiotherapy and oncology, 194(1), S821-S822. Elsevier

Mahapatra, Dwarikanath; Bozorgtabar, Behzad; Ge, Zongyuan; Reyes, Mauricio (2024). GANDALF: Graph-based transformer and Data Augmentation Active Learning Framework with interpretable features for multi-label chest Xray classification. Medical image analysis, 93(103075), p. 103075. Elsevier 10.1016/j.media.2023.103075

Alwan, Louhai; Benz, Dominik C; Cuddy, Sarah A M; Dobner, Stephan; Shiri, Isaac; Caobelli, Federico; Bernhard, Benedikt; Stämpfli, Simon F; Eberli, Franz; Reyes, Mauricio; Kwong, Raymond Y; Falk, Rodney H; Dorbala, Sharmila; Gräni, Christoph (2024). Current and Evolving Multimodality Cardiac Imaging in Managing Transthyretin Amyloid Cardiomyopathy. JACC. Cardiovascular imaging, 17(2), pp. 195-211. Elsevier 10.1016/j.jcmg.2023.10.010

Maier-Hein, Lena; Reinke, Annika; Godau, Patrick; Tizabi, Minu D; Buettner, Florian; Christodoulou, Evangelia; Glocker, Ben; Isensee, Fabian; Kleesiek, Jens; Kozubek, Michal; Reyes, Mauricio; Riegler, Michael A; Wiesenfarth, Manuel; Kavur, A Emre; Sudre, Carole H; Baumgartner, Michael; Eisenmann, Matthias; Heckmann-Nötzel, Doreen; Rädsch, Tim; Acion, Laura; ... (2024). Metrics reloaded: recommendations for image analysis validation. Nature methods, 21(2), pp. 195-212. Nature Publishing Group 10.1038/s41592-023-02151-z

Reinke, Annika; Tizabi, Minu D; Baumgartner, Michael; Eisenmann, Matthias; Heckmann-Nötzel, Doreen; Kavur, A Emre; Rädsch, Tim; Sudre, Carole H; Acion, Laura; Antonelli, Michela; Arbel, Tal; Bakas, Spyridon; Benis, Arriel; Buettner, Florian; Cardoso, M Jorge; Cheplygina, Veronika; Chen, Jianxu; Christodoulou, Evangelia; Cimini, Beth A; Farahani, Keyvan; ... (2024). Understanding metric-related pitfalls in image analysis validation. Nature methods, 21(2), pp. 182-194. Nature Publishing Group 10.1038/s41592-023-02150-0

You, Suhang; Wiest, Roland; Reyes, Mauricio (2024). SaRF: Saliency regularized feature learning improves MRI sequence classification. Computer methods and programs in biomedicine, 243(107867), p. 107867. Elsevier 10.1016/j.cmpb.2023.107867

Garcia Henao, John Anderson; Depotter, Arno; Bower, Danielle V; Bajercius, Herkus; Todorova, Plamena Teodosieva; Saint-James, Hugo; de Mortanges, Aurélie Pahud; Barroso, Maria Cecilia; He, Jianchun; Yang, Junlin; You, Chenyu; Staib, Lawrence H; Gange, Christopher; Ledda, Roberta Eufrasia; Caminiti, Caterina; Silva, Mario; Cortopassi, Isabel Oliva; Dela Cruz, Charles S; Hautz, Wolf; Bonel, Harald M; ... (2023). A Multiclass Radiomics Method-Based WHO Severity Scale for Improving COVID-19 Patient Assessment and Disease Characterization From CT Scans. Investigative radiology, 58(12), pp. 882-893. Wolters Kluwer Health 10.1097/RLI.0000000000001005

Mahapatra, Dwarikanath; Jimeno Yepes, Antonio Jose; Kuanar, Shiba; Roy, Sudipta; Bozorgtabar, Behzad; Reyes, Mauricio; Ge, Zongyuan (8 October 2023). Class Specific Feature Disentanglement and Text Embeddings for Multi-label Generalized Zero Shot CXR Classification. In: International Conference on Medical Image Computing and Computer-Assisted Intervention. Lecture Notes in Computer Science: Vol. 14221 (pp. 276-286). Springer 10.1007/978-3-031-43895-0_26

Kamath, Amith; Willmann, Jonas; Andratschke, Nicolaus; Reyes, Mauricio (8 October 2023). Do We Really Need that Skip-Connection? Understanding Its Interplay with Task Complexity. In: International Conference on Medical Image Computing and Computer-Assisted Intervention. Lecture Notes in Computer Science: Vol. 14223 (pp. 302-311). Springer 10.1007/978-3-031-43901-8_29

Gassner, Mathias; Barranco Garcia, Javier; Tanadini-Lang, Stephanie; Bertoldo, Fabio; Fröhlich, Fabienne; Guckenberger, Matthias; Haueis, Silvia; Pelzer, Christin; Reyes, Mauricio; Schmithausen, Patrick; Simic, Dario; Staeger, Ramon; Verardi, Fabio; Andratschke, Nicolaus; Adelmann, Andreas; Braun, Ralph P (2023). Saliency-Enhanced Content-Based Image Retrieval for Diagnosis Support in Dermatology Consultation: Reader Study. JMIR dermatology, 6(e42129), e42129. JMIR Publications 10.2196/42129

Ocaña-Tienda, Beatriz; Pérez-Beteta, Julián; Villanueva-García, José D; Romero-Rosales, José A; Molina-García, David; Suter, Yannick; Asenjo, Beatriz; Albillo, David; Ortiz de Mendivil, Ana; Pérez-Romasanta, Luis A; González-Del Portillo, Elisabet; Llorente, Manuel; Carballo, Natalia; Nagib-Raya, Fátima; Vidal-Denis, Maria; Luque, Belén; Reyes, Mauricio; Arana, Estanislao; Pérez-García, Víctor M (2023). A comprehensive dataset of annotated brain metastasis MR images with clinical and radiomic data. Scientific data, 10(1), p. 208. 10.1038/s41597-023-02123-0

Rüfenacht, Elias; Kamath, Amith; Suter, Yannick; Poel, Robert; Ermiş, Ekin; Scheib, Stefan; Reyes, Mauricio (2023). PyRaDiSe: A Python package for DICOM-RT-based auto-segmentation pipeline construction and DICOM-RT data conversion. Computer methods and programs in biomedicine, 231(107374), p. 107374. Elsevier 10.1016/j.cmpb.2023.107374

Mahapatra, Dwarikanath; Poellinger, Alexander; Reyes, Mauricio (2023). Graph Node Based Interpretability Guided Sample Selection for Active Learning. IEEE transactions on medical imaging, 42(3), pp. 661-673. Institute of Electrical and Electronics Engineers IEEE 10.1109/TMI.2022.3215017

Rebsamen, Michael; McKinley, Richard; Radojewski, Piotr; Pistor, Maximilian; Friedli, Christoph; Hoepner, Robert; Salmen, Anke; Chan, Andrew; Reyes, Mauricio; Wagner, Franca; Wiest, Roland; Rummel, Christian (2023). Reliable brain morphometry from contrast-enhanced T1w-MRI in patients with multiple sclerosis. Human brain mapping, 44(3), pp. 970-979. Wiley-Blackwell 10.1002/hbm.26117

Silva, Wilson; Gonçalves, Tiago; Härmä, Kirsi; Schröder, Erich; Obmann, Verena Carola; Barroso, María Cecilia; Pöllinger, Alexander; Reyes, Mauricio; Cardoso, Jaime S (2023). Author Correction: Computer-aided diagnosis through medical image retrieval in radiology. Scientific reports, 13(1), p. 1470. Springer Nature 10.1038/s41598-023-28523-1

Pati, Sarthak; Baid, Ujjwal; Edwards, Brandon; Sheller, Micah; Wang, Shih-Han; Reina, G Anthony; Foley, Patrick; Gruzdev, Alexey; Karkada, Deepthi; Davatzikos, Christos; Sako, Chiharu; Ghodasara, Satyam; Bilello, Michel; Mohan, Suyash; Vollmuth, Philipp; Brugnara, Gianluca; Preetha, Chandrakanth J; Sahm, Felix; Maier-Hein, Klaus; Zenk, Maximilian; ... (2023). Author Correction: Federated learning enables big data for rare cancer boundary detection. Nature communications, 14(1), p. 436. Nature Publishing Group 10.1038/s41467-023-36188-7

Krcek, Reinhardt; Poel, Robert; Hemmatazad, Hossein; Reyes, Mauricio; Ermis, Ekin (17 January 2023). Variations in contouring brain target volumes and Organs at Risk on 3 T vs. 7 T MRI: An intra-rater/inter-rater analysis study. Strahlentherapie und Onkologie, p. 215. Springer

Abayazeed, Aly H; Abbassy, Ahmed; Müeller, Michael; Hill, Michael; Qayati, Mohamed; Mohamed, Shady; Mekhaimar, Mahmoud; Raymond, Catalina; Dubey, Prachi; Nael, Kambiz; Rohatgi, Saurabh; Kapare, Vaishali; Kulkarni, Ashwini; Shiang, Tina; Kumar, Atul; Andratschke, Nicolaus; Willmann, Jonas; Brawanski, Alexander; De Jesus, Reordan; Tuna, Ibrahim; ... (2023). NS-HGlio: A generalizable and repeatable HGG segmentation and volumetric measurement AI algorithm for the longitudinal MRI assessment to inform RANO in trials and clinics. Neuro-oncology advances, 5(1), vdac184. Oxford University Press 10.1093/noajnl/vdac184

Poel, Robert; Kamath, Amith J.; Willmann, Jonas; Andratschke, Nicolaus; Ermis, Ekin; Aebersold, Daniel M.; Manser, Peter; Reyes, Mauricio (2023). Deep-Learning-Based Dose Predictor for Glioblastoma–Assessing the Sensitivity and Robustness for Dose Awareness in Contouring. Cancers, 15(17) MDPI AG 10.3390/cancers15174226

Suter, Yannick; Notter, Michelle; Meier, Raphael; Loosli, Tina; Schucht, Philippe; Wiest, Roland; Reyes, Mauricio; Knecht, Urspeter (2023). Evaluating automated longitudinal tumor measurements for glioblastoma response assessment. Frontiers in radiology, 3(1211859), p. 1211859. Frontiers Media 10.3389/fradi.2023.1211859

Kamath, Amith; Poel, Robert; Willmann, Jonas; Andratschke, Nicolaus; Reyes, Mauricio (2023). How Sensitive Are Deep Learning Based Radiotherapy Dose Prediction Models To Variability In Organs At Risk Segmentation? In: 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI) (pp. 1-4). IEEE 10.1109/ISBI53787.2023.10230559

You, Suhang; Tomar, Devavrat; Bozorgtabar, Behzad; Reyes, Mauricio (2023). Sagtta: saliency guided test time augmentation for medical image segmentation across vendor domain shift. In: 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI). IEEE, 2023. 10.1109/ISBI53787.2023.10230764

Reyes, Mauricio (2023). MedShapeNet--A Large-Scale Dataset of 3D Medical Shapes for Computer Vision (arXiv). Cornell University

Rüfenacht, Elias; Poel, Robert; Kamath, Amith; Ermis, Ekin; Scheib, Stefan; Fix, Michael K.; Reyes, Mauricio (2023). Dose Guidance for Radiotherapy-Oriented Deep Learning Segmentation. Lecture notes in computer science, 14228, pp. 525-534. Cham: Springer 10.1007/978-3-031-43996-4_50

Kamath, Amith; Poel, Robert; Willmann, Jonas; Ermis, Ekin; Andratschke, Nicolaus; Reyes, Mauricio (2023). ASTRA: Atomic Surface Transformations for Radiotherapy Quality Assurance. In: 2023 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC) (pp. 1-4). IEEE 10.1109/EMBC40787.2023.10341062

Suter, Yannick; Knecht, Urspeter; Valenzuela, Waldo; Notter, Michelle; Hewer, Ekkehard; Schucht, Philippe; Wiest, Roland; Reyes, Mauricio (2022). The LUMIERE dataset: Longitudinal Glioblastoma MRI with expert RANO evaluation. Scientific data, 9(1), p. 768. Nature Publishing Group 10.1038/s41597-022-01881-7

Hernandez Petzsche, Moritz R; de la Rosa, Ezequiel; Hanning, Uta; Wiest, Roland; Valenzuela, Waldo; Reyes, Mauricio; Meyer, Maria; Liew, Sook-Lei; Kofler, Florian; Ezhov, Ivan; Robben, David; Hutton, Alexandre; Friedrich, Tassilo; Zarth, Teresa; Bürkle, Johannes; Baran, The Anh; Menze, Björn; Broocks, Gabriel; Meyer, Lukas; Zimmer, Claus; ... (2022). ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset. Scientific data, 9(1), p. 762. Nature Publishing Group 10.1038/s41597-022-01875-5

Pati, Sarthak; Baid, Ujjwal; Edwards, Brandon; Sheller, Micah; Wang, Shih-Han; Reina, G Anthony; Foley, Patrick; Gruzdev, Alexey; Karkada, Deepthi; Davatzikos, Christos; Sako, Chiharu; Ghodasara, Satyam; Bilello, Michel; Mohan, Suyash; Vollmuth, Philipp; Brugnara, Gianluca; Preetha, Chandrakanth J; Sahm, Felix; Maier-Hein, Klaus; Zenk, Maximilian; ... (2022). Federated learning enables big data for rare cancer boundary detection. Nature communications, 13(1), p. 7346. Nature Publishing Group 10.1038/s41467-022-33407-5

Silva, Wilson; Gonçalves, Tiago; Härmä, Kirsi; Schröder, Erich; Obmann, Verena Carola; Barroso, Maria Cecilia; Poellinger, Alexander; Reyes, Mauricio; Cardoso, Jaime S (2022). Computer-aided diagnosis through medical image retrieval in radiology. Scientific reports, 12(1), p. 20732. Springer Nature 10.1038/s41598-022-25027-2

You, Suhang; Reyes, Mauricio (2022). Influence of contrast and texture based image modifications on the performance and attention shift of U-Net models for brain tissue segmentation. Frontiers in neuroimaging, 1(1012639), p. 1012639. Frontiers 10.3389/fnimg.2022.1012639

Poel, Robert; Rüfenacht, Elias; Ermis, Ekin; Müller, Michael; Fix, Michael K; Aebersold, Daniel M; Manser, Peter; Reyes, Mauricio (2022). Impact of random outliers in auto-segmented targets on radiotherapy treatment plans for glioblastoma. Radiation oncology, 17(1), p. 170. BioMed Central 10.1186/s13014-022-02137-9

Mahapatra, Dwarikanath; Poellinger, Alexander; Reyes, Mauricio (2022). Interpretability-Guided Inductive Bias For Deep Learning Based Medical Image. Medical image analysis, 81, p. 102551. Elsevier 10.1016/j.media.2022.102551

Liew, Sook-Lei; Lo, Bethany P; Donnelly, Miranda R; Zavaliangos-Petropulu, Artemis; Jeong, Jessica N; Barisano, Giuseppe; Hutton, Alexandre; Simon, Julia P; Juliano, Julia M; Suri, Anisha; Wang, Zhizhuo; Abdullah, Aisha; Kim, Jun; Ard, Tyler; Banaj, Nerisa; Borich, Michael R; Boyd, Lara A; Brodtmann, Amy; Buetefisch, Cathrin M; Cao, Lei; ... (2022). A large, curated, open-source stroke neuroimaging dataset to improve lesion segmentation algorithms. Scientific data, 9(1), p. 320. Nature Publishing Group 10.1038/s41597-022-01401-7

Kang, Miao; Hu, Xiaojun; Huang, Weilin; Scott, Matthew R; Reyes, Mauricio (2022). Dual-stream pyramid registration network. Medical image analysis, 78, p. 102379. Elsevier 10.1016/j.media.2022.102379

Rebsamen, Michael; Radojewski, Piotr; McKinley, Richard; Reyes, Mauricio; Wiest, Roland; Rummel, Christian (2022). A Quantitative Imaging Biomarker Supporting Radiological Assessment of Hippocampal Sclerosis Derived From Deep Learning-Based Segmentation of T1w-MRI. Frontiers in neurology, 13, p. 812432. Frontiers Media S.A. 10.3389/fneur.2022.812432

Rizzo, Rudy; Dziadosz, Martyna; Kyathanahally, Sreenath P.; Reyes, Mauricio; Kreis, Roland (2022). Reliability of Quantification Estimates in MR Spectroscopy: CNNs vs Traditional Model Fitting. Lecture notes in computer science, 13438, pp. 715-724. Springer 10.1007/978-3-031-16452-1_68

Mahapatra, Dwarikanath; Poellinger, Alexander; Shao, Ling; Reyes, Mauricio (2021). Interpretability-Driven Sample Selection Using Self Supervised Learning For Disease Classification And Segmentation. IEEE transactions on medical imaging, 40(10), pp. 2548-2562. Institute of Electrical and Electronics Engineers IEEE 10.1109/TMI.2021.3061724

Poel, Robert; Rüfenacht, Elias; Herrmann, Evelyn; Scheib, Stefan; Manser, Peter; Aebersold, Daniel M.; Reyes, Mauricio (2021). The predictive value of segmentation metrics on dosimetry in organs at risk of the brain. Medical image analysis, 73, p. 102161. Elsevier 10.1016/j.media.2021.102161

Hakim, Arsany; Christensen, Søren; Winzeck, Stefan; Lansberg, Maarten G; Parsons, Mark W; Lucas, Christian; Robben, David; Wiest, Roland; Reyes, Mauricio; Zaharchuk, Greg (2021). Predicting Infarct Core From Computed Tomography Perfusion in Acute Ischemia With Machine Learning: Lessons From the ISLES Challenge. Stroke, 52(7), pp. 2328-2337. Wolters Kluwer Health 10.1161/STROKEAHA.120.030696

Pinto, Adriano; Pereira, Sérgio; Meier, Raphael; Wiest, Roland; Alves, Victor; Reyes, Mauricio; Silva, Carlos A (2021). Combining unsupervised and supervised learning for predicting the final stroke lesion. Medical image analysis, 69(101888), p. 101888. Elsevier 10.1016/j.media.2020.101888

Menze, Bjoern; Isensee, Fabian; Wiest, Roland; Wiestler, Bene; Maier-Hein, Klaus; Reyes, Mauricio; Bakas, Spyridon (2021). Analyzing Magnetic Resonance Imaging Data from Glioma Patients using Deep Learning. Computerized medical imaging and graphics, 88, p. 101828. Elsevier 10.1016/j.compmedimag.2020.101828

McKinley, Richard; Wepfer, Rik; Aschwanden, Fabian; Grunder, Lorenz; Muri, Raphaela; Rummel, Christian; Verma, Rajeev; Weisstanner, Christian; Reyes, Mauricio; Salmen, Anke; Chan, Andrew; Wagner, Franca; Wiest, Roland (2021). Simultaneous lesion and brain segmentation in multiple sclerosis using deep neural networks. Scientific reports, 11(1), p. 1087. Springer Nature 10.1038/s41598-020-79925-4

Jungo, Alain; Scheidegger, Olivier; Reyes, Mauricio; Balsiger, Fabian (2021). pymia: A Python package for data handling and evaluation in deep learning-based medical image analysis. Computer methods and programs in biomedicine, 198, p. 105796. Elsevier 10.1016/j.cmpb.2020.105796

Suter, Yannick; Knecht, Urspeter; Wiest, Roland; Reyes, Mauricio (2021). Overall Survival Prediction for Glioblastoma on Pre-treatment MRI Using Robust Radiomics and Priors. Lecture notes in computer science, 12658, pp. 307-317. Springer 10.1007/978-3-030-72084-1_28

Rebsamen, Michael; Rummel, Christian; Reyes, Mauricio; Wiest, Roland; McKinley, Richard (2020). Direct cortical thickness estimation using deep learning-based anatomy segmentation and cortex parcellation. Human brain mapping, 41(17), pp. 4804-4814. Wiley-Blackwell 10.1002/hbm.25159

Balsiger, Fabian; Jungo, Alain; Scheidegger, Olivier; Marty, Benjamin; Reyes, Mauricio (2020). Learning Bloch Simulations for MR Fingerprinting by Invertible Neural Networks. In: Deeba, Farah; Johnson, Patricia; Würfl, Tobias; Ye, Jong Chul (eds.) Machine Learning for Medical Image Reconstruction. Lecture Notes in Computer Science: Vol. 12450 (pp. 60-69). Cham: Springer 10.1007/978-3-030-61598-7_6

Suter, Yannick; Knecht, Urspeter; Alao, Mariana; Valenzuela, Waldo; Hewer, Ekkehard; Schucht, Philippe; Wiest, Roland; Reyes, Mauricio (2020). Radiomics for glioblastoma survival analysis in pre-operative MRI: exploring feature robustness, class boundaries, and machine learning techniques. Cancer imaging : the official publication of the International Cancer Imaging Society, 20(55), pp. 1-13. BioMed Central 10.1186/s40644-020-00329-8

Balsiger, Fabian; Jungo, Alain; Scheidegger, Olivier; Carlier, Pierre G; Reyes, Mauricio; Marty, Benjamin (2020). Spatially regularized parametric map reconstruction for fast magnetic resonance fingerprinting. Medical image analysis, 64(101741), p. 101741. Elsevier 10.1016/j.media.2020.101741

Reyes, Mauricio; Meier, Raphael; Pereira, Sérgio; Silva, Carlos A; Dahlweid, Fried-Michael; von Tengg-Kobligk, Hendrik; Summers, Ronald M; Wiest, Roland (2020). On the Interpretability of Artificial Intelligence in Radiology: Challenges and Opportunities. Radiology: artificial intelligence, 2(3), e190043. Radiological Society of North America 10.1148/ryai.2020190043

Ermis, Ekin; Jungo, Alain; Poel, Robert; Blatti-Moreno, Marcela; Meier, Raphael; Knecht, Urspeter; Aebersold, Daniel M.; Fix, Michael K.; Manser, Peter; Reyes, Mauricio; Herrmann, Evelyn (2020). Fully automated brain resection cavity delineation for radiation target volume definition in glioblastoma patients using deep learning. Radiation oncology, 15(1), p. 100. BioMed Central 10.1186/s13014-020-01553-z

Jungo, Alain; Balsiger, Fabian; Reyes, Mauricio (2020). Analyzing the Quality and Challenges of Uncertainty Estimations for Brain Tumor Segmentation. Frontiers in neuroscience, 14(282), p. 282. Frontiers Research Foundation 10.3389/fnins.2020.00282

Rebsamen, Michael; Suter, Yannick; Wiest, Roland; Reyes, Mauricio; Rummel, Christian (2020). Brain Morphometry Estimation: From Hours to Seconds Using Deep Learning. Frontiers in neurology, 11(244), p. 244. Frontiers Media S.A. 10.3389/fneur.2020.00244

Hu, Xiaojun; Luo, Weijian; Hu, Jiliang; Guo, Sheng; Huang, Weilin; Scott, Matthew R; Wiest, Roland; Dahlweid, Michael; Reyes, Mauricio (2020). Brain SegNet: 3D local refinement network for brain lesion segmentation. BMC medical imaging, 20(1), p. 17. BioMed Central 10.1186/s12880-020-0409-2

McKinley, Richard; Wepfer, Rik; Grunder, Lorenz; Aschwanden, Fabian; Fischer, Tim; Friedli, Christoph; Muri, Raphaela; Rummel, Christian; Verma, Rajeev Kumar; Weisstanner, Christian; Wiestler, Benedikt; Berger, Christoph; Eichinger, Paul; Muehlau, Mark; Reyes, Mauricio; Salmen, Anke; Chan, Andrew; Wiest, Roland; Wagner, Franca (2020). Automatic detection of lesion load change in Multiple Sclerosis using convolutional neural networks with segmentation confidence. NeuroImage: Clinical, 25, p. 102104. Elsevier 10.1016/j.nicl.2019.102104

McKinley, Richard; Wepfer, Rik; Aschwanden, Fabian; Grunder, Lorenz; Muri, Raphaela; Rummel, Christian; Verma, Rajeev; Weisstanner, Christian; Reyes, Mauricio; Salmen, Anke; Chan, Andrew; Wagner, Franca; Wiest, Roland (2020). Robustness of Simultaneous Lesion and Neuroanatomy Segmentation in Multiple Sclerosis Using Deep Neural Networks (In Press). SSRN Electronic Journal Elsevier 10.2139/ssrn.3529469

Jin, Baudouin Zongxin; De Stefano, Pia; Petroulia, Valentina; Rummel, Christian; Kiefer, Claus; Reyes, Mauricio; Schindler, Kaspar; van Mierlo, Pieter; Seeck, Margitta; Wiest, Roland (2020). Diagnosis of epilepsy after first seizure. Introducing the SWISS FIRST study. Clinical and translational neuroscience, 4(2), 2514183X2093944. Sage Publications 10.1177/2514183X20939448

Silva, Wilson; Pöllinger, Alexander; Cardoso, Jaime S.; Reyes, Mauricio (2020). Interpretability-Guided Content-Based Medical Image Retrieval. Lecture notes in computer science, 12261, pp. 305-314. Cham: Springer 10.1007/978-3-030-59710-8_30

Rüfenacht, Elias; Jungo, Alain; Ermis, Ekin; Hemmatazad, Hossein; Blatti, Marcela Judith; Aebersold, Daniel; Manser, Peter; Fix, Michael; Reyes, Mauricio; Herrmann, Evelyn (December 2019). Fully automated organs at risk delineation for brain tumor radiation planning in patients with glioblastoma using deep learning. Strahlentherapie und Onkologie, 195(12), p. 1149. Berlin Heidelberg: Springer

Da Silva Mendes Pedrosa de Barros, Nuno Miguel; Meier, Raphael; Pletscher, Martin; Stettler, Samuel; Knecht, Urspeter; Reyes, Mauricio; Gralla, Jan; Wiest, Roland; Slotboom, Johannes (2019). Analysis of metabolic abnormalities in high-grade glioma using MRSI and convex NMF. NMR in biomedicine, 32(8), e4109. Wiley Interscience 10.1002/nbm.4109

Suter, Yannick Raphael; Jungo, Alain; Rebsamen, Michael; Knecht, Urspeter; Herrmann, Evelyn; Wiest, Roland; Reyes, Mauricio (26 January 2019). Deep Learning Versus Classical Regression for Brain Tumor Patient Survival Prediction. Lecture notes in computer science, 11384, pp. 429-440. Cham: Springer 10.1007/978-3-030-11726-9_38

Meier, Raphael; Lux, Paula; Jung, Simon; Fischer, Urs; Gralla, Jan; Reyes, Mauricio; Wiest, Roland; McKinley, Richard; Kaesmacher, Johannes (2019). Neural network-derived perfusion Maps for the assessment of lesions in patients with acute ischemic stroke (Submitted). Radiology: artificial intelligence Radiological Society of North America 10.1148/ryai.2019190019

Rebsamen, Michael; Knecht, Urspeter; Reyes, Mauricio; Wiest, Roland; Meier, Raphael; McKinley, Richard (2019). Divide and Conquer: Stratifying Training Data by Tumor Grade Improves Deep Learning-Based Brain Tumor Segmentation. Frontiers in neuroscience, 13, p. 1182. Frontiers Research Foundation 10.3389/fnins.2019.01182

McKinley, Richard; Grunder, Lorenz; Wepfer, Rik; Aschwanden, Fabian; Fischer, Tim; Friedli, Christoph; Muri, Raphaela; Rummel, Christian; Verma, Rajeev; Weisstanner, Christian; Reyes, Mauricio; Salmen, Anke; Chan, Andrew; Wiest, Roland; Wagner, Franca (2019). Automatic detection of lesion load change in Multiple Sclerosis using convolutional neural networks with segmentation confidence (arXiv). Cornell University

Balsiger, Fabian; Soom, Yannick; Scheidegger, Olivier; Reyes, Mauricio (2019). Learning Shape Representation on Sparse Point Clouds for Volumetric Image Segmentation. In: Medical Image Computing and Computer Assisted Intervention – MICCAI 2019. Lecture Notes in Computer Science: Vol. 11765 (pp. 273-281). Cham: Springer International Publishing 10.1007/978-3-030-32245-8_31

Jungo, Alain; Reyes, Mauricio (2019). Assessing Reliability and Challenges of Uncertainty Estimations for Medical Image Segmentation. Lecture notes in computer science, 11765, pp. 48-56. Springer 10.1007/978-3-030-32245-8_6

Chandran, Vimal; Maquer, Ghislain Bernard; Gerig, Thomas; Zysset, Philippe; Reyes, Mauricio (2019). Supervised learning for bone shape and cortical thickness estimation from CT images for finite element analysis. Medical image analysis, 52, pp. 42-55. Elsevier 10.1016/j.media.2018.11.001

Rüfenacht, Elias; Jungo, Alain; Ermis, Ekin; Blatti-Moreno, Marcela; Hemmatazad, Hossein; Aebersold, Daniel M.; Fix, Michael; Manser, Peter; Reyes, Mauricio; Herrmann, Evelyn (2019). Organs at Risk Delineation for Brain Tumor Radiation Planning in Patients with Glioblastoma Using Deep Learning. International journal of radiation oncology, biology, physics, 105(1), E718-E719. Elsevier 10.1016/j.ijrobp.2019.06.892

da Silva Mendes Pedrosa de Barros, Nuno Miguel; Meier, Raphael; Pletscher, Martin; Stettler, Samuel; Knecht, Urspeter; Herrmann, Evelyn; Schucht, Philippe; Reyes, Mauricio; Gralla, Jan; Wiest, Roland; Slotboom, Johannes (2018). On the relation between MR spectroscopy features and the distance to MRI-visible solid tumor in GBM patients. Magnetic resonance in medicine, 80(6), pp. 2339-2355. Wiley-Liss 10.1002/mrm.27359

Hlushchuk, Ruslan; Zubler, Cédric; Barré, Sébastien; Correa Shokiche, Carlos Enrique; Schaad, Laura; Röthlisberger, Raphael; Wnuk, Monika L; Daniel, Christoph; Khoma, Oleksiy-Zakhar; Tschanz, Stefan A.; Reyes, Mauricio; Djonov, Valentin (2018). Cutting-edge microangio-CT: new dimensions in vascular imaging and kidney morphometry. American journal of physiology - renal physiology, 314(3), F493-F499. American Physiological Society 10.1152/ajprenal.00099.2017

Kjer, H Martin; Fagertun, Jens; Wimmer, Wilhelm; Gerber, Nicolas; Vera, Sergio; Barazzetti, Livia; Mangado, Nerea; Ceresa, Mario; Piella, Gemma; Stark, Thomas; Stauber, Martin; Reyes, Mauricio; Weber, Stefan; Caversaccio, Marco; González Ballester, Miguel Ángel; Paulsen, Rasmus R (2018). Patient-specific estimation of detailed cochlear shape from clinical CT images. International Journal of Computer Assisted Radiology and Surgery, 13(3), pp. 389-396. Springer 10.1007/s11548-017-1701-7

Lu, Ping; Barazzetti, Livia; Chandran, Vimal; Gerber, Kate; Weber, Stefan; Gerber, Nicolas; Reyes, Mauricio (2018). Highly accurate Facial Nerve Segmentation Refinement from CBCT/CT Imaging using a Super Resolution Classification Approach. IEEE transactions on biomedical engineering, 65(1), pp. 178-188. Institute of Electrical and Electronics Engineers IEEE 10.1109/TBME.2017.2697916

Habegger, Simon; Wiest, Roland; Weder, Bruno; Mordasini, Pasquale; Gralla, Jan; Häni, Levin; Jung, Simon; Reyes, Mauricio; McKinley, Richard (2018). Relating Acute Lesion Loads to Chronic Outcome in Ischemic Stroke-An Exploratory Comparison of Mismatch Patterns and Predictive Modeling. Frontiers in neurology, 9(737), p. 737. Frontiers Media S.A. 10.3389/fneur.2018.00737

Balsiger, Fabian; Steindel, Carolin; Arn, Mirjam; Wagner, Benedikt; Grunder, Lorenz Nicolas; El-Koussy, Marwan; Valenzuela, Waldo Enrique; Reyes, Mauricio; Scheidegger, Olivier (2018). Segmentation of Peripheral Nerves From Magnetic Resonance Neurography: A Fully-Automatic, Deep Learning-Based Approach. Frontiers in neurology, 9(777), p. 777. Frontiers Media S.A. 10.3389/fneur.2018.00777

Pinto, Adriano; McKinley, Richard; Alves, Victor; Wiest, Roland; Silva, Carlos A; Reyes, Mauricio (2018). Stroke Lesion Outcome Prediction Based on MRI Imaging Combined With Clinical Information. Frontiers in neurology, 9(1060), p. 1060. Frontiers Media S.A. 10.3389/fneur.2018.01060

Mahapatra, Dwarikanath; Bozorgtabar, Behzad; Thiran, Jean-Philippe; Reyes, Mauricio (2018). Efficient Active Learning for Image Classification and Segmentation Using a Sample Selection and Conditional Generative Adversarial Network. In: Frangi, Alejandro F.; Schnabel, Julia A.; Davatzikos, Christos; Alberola-López, Carlos; Fichtinger, Gabor (eds.) Medical Image Computing and Computer Assisted Interventions. Lecture Notes in Computer Science: Vol. 11071 (pp. 580-588). Cham: Springer International Publishing 10.1007/978-3-030-00934-2_65

Pinto, Adriano; Pereira, Sérgio; Meier, Raphael; Alves, Victor; Wiest, Roland; Silva, Carlos A.; Reyes, Mauricio (2018). Enhancing Clinical MRI Perfusion Maps with Data-Driven Maps of Complementary Nature for Lesion Outcome Prediction. In: Frangi, Alejandro F.; Schnabel, Julia A.; Davatzikos, Christos; Alberola-López, Carlos; Fichtinger, Gabor (eds.) Medical Image Computing and Computer Assisted Interventions. Lecture Notes in Computer Science: Vol. 11072 (pp. 107-115). Cham: Springer International Publishing 10.1007/978-3-030-00931-1_13

Pereira, Sérgio; Meier, Raphael; Alves, Victor; Reyes, Mauricio; Silva, Carlos A. (2018). Automatic Brain Tumor Grading from MRI Data Using Convolutional Neural Networks and Quality Assessment. In: Understanding and Interpreting Machine Learning in Medical Image Computing Applications. Lecture Notes in Computer Science: Vol. 11038 (pp. 106-114). Cham: Springer International Publishing 10.1007/978-3-030-02628-8_12

Pereira, Sérgio; Meier, Raphael; McKinley, Richard; Wiest, Roland; Alves, Victor; Silva, Carlos A; Reyes, Mauricio (2018). Enhancing interpretability of automatically extracted machine learning features: application to a RBM-Random Forest system on brain lesion segmentation. Medical image analysis, 44, pp. 228-244. Elsevier 10.1016/j.media.2017.12.009

Winzeck, Stefan; Hakim, Arsany; McKinley, Richard; Pinto, José A A D S R; Alves, Victor; Silva, Carlos; Pisov, Maxim; Krivov, Egor; Belyaev, Mikhail; Monteiro, Miguel; Oliveira, Arlindo; Choi, Youngwon; Paik, Myunghee Cho; Kwon, Yongchan; Lee, Hanbyul; Kim, Beom Joon; Won, Joong-Ho; Islam, Mobarakol; Ren, Hongliang; Robben, David; ... (2018). ISLES 2016 and 2017-Benchmarking Ischemic Stroke Lesion Outcome Prediction Based on Multispectral MRI. Frontiers in neurology, 9(679), p. 679. Frontiers Media S.A. 10.3389/fneur.2018.00679

Balsiger, Fabian; Shridhar Konar, Amaresha; Chikop, Shivaprasad; Chandran, Vimal; Scheidegger, Olivier; Geethanath, Sairam; Reyes, Mauricio (2018). Magnetic Resonance Fingerprinting Reconstruction via Spatiotemporal Convolutional Neural Networks. In: Machine Learning for Medical Image Reconstruction. Lecture Notes in Computer Science: Vol. 11074 (pp. 39-46). Cham: Springer International Publishing 10.1007/978-3-030-00129-2_5

Herrmann, Evelyn; Ermis, Ekin; Meier, R.; Blatti-Moreno, Marcela; Knecht, U.P.; Aebersold, Daniel; Manser, Peter; Reyes, Mauricio (2018). Fully Automated Segmentation of the Brain Resection Cavity for Radiation Target Volume Definition in Glioblastoma Patients. International journal of radiation oncology, biology, physics, 102(3), S194. Elsevier 10.1016/j.ijrobp.2018.07.087

Suter, Yannick Raphael; Rummel, Christian; Wiest, Roland; Reyes, Mauricio (2018). Fast and uncertainty-aware cerebral cortex morphometry estimation using random forest regression. In: 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018) (pp. 1052-1055). IEEE 10.1109/ISBI.2018.8363752

Jungo, Alain; Meier, Raphael; Ermis, Ekin; Herrmann, Evelyn; Reyes, Mauricio (2018). Uncertainty-driven Sanity Check: Application to Postoperative Brain Tumor Cavity Segmentation. In: International Conference on Medical Imaging with Deep Learning. 04-06.07.2018.

Jungo, Alain; McKinley, Richard; Meier, Raphael; Knecht, Urspeter; Vera, Luis; Pérez-Beteta, Julián; Molina-García, David; Pérez-García, Víctor M.; Wiest, Roland; Reyes, Mauricio (2018). Towards uncertainty-assisted brain tumor segmentation and survival prediction. In: International Conference On Medical Image Computing & Computer Assisted Intervention. 10.1007/978-3-319-75238-9_40

Jungo, Alain; Meier, Raphael; Ermis, Ekin; Blatti-Moreno, Marcela; Herrmann, Evelyn; Wiest, Roland; Reyes, Mauricio (2018). On the Effect of Inter-observer Variability for a Reliable Estimation of Uncertainty of Medical Image Segmentation. In: International Conference on Medical Image Computing and Computer-Assisted Intervention. Lecture Notes in Computer Science: Vol. 11070 (pp. 682-690). Springer 10.1007/978-3-030-00928-1_77

Kellner-Weldon, Frauke; Stippich, Christoph; Wiest, Roland; Lehmann, Vera; Meier, Raphael; Beck, Jürgen; Schucht, Philippe; Raabe, Andreas; Reyes, Mauricio; Bink, Andrea (2017). Comparison of perioperative automated versus manual two-dimensional tumor analysis in glioblastoma patients. European journal of radiology, 95, pp. 75-81. Elsevier 10.1016/j.ejrad.2017.07.028

Taghizadeh, Elham; Chandran, Vimal; Reyes, Mauricio; Zysset, Philippe; Büchler, Philippe (2017). Statistical analysis of the inter-individual variations of the bone shape, volume fraction and fabric and their correlations in the proximal femur. Bone, 103, pp. 252-261. Elsevier 10.1016/j.bone.2017.07.012

Meier, Raphael; Porz, Nicole; Knecht, Urspeter; Schucht, Philippe; Beck, Jürgen; Slotboom, Johannes; Wiest, Roland; Reyes, Mauricio (2017). Automatic estimation of extent of resection and residual tumor volume of patients with glioblastoma. Journal of neurosurgery, 127(4), pp. 798-806. American Association of Neurological Surgeons 10.3171/2016.9.JNS16146

Gerber, Nicolas; Reyes, Mauricio; Barazzetti, Livia; Kjer, Hans Martin; Vera, Sergio; Stauber, Martin; Mistrik, Pavel; Ceresa, Mario; Mangado, Nerea; Wimmer, Wilhelm; Stark, Thomas; Paulsen, Rasmus R.; Weber, Stefan; Caversaccio, Marco; Ballester, Miguel A. González (2017). A multiscale imaging and modelling dataset of the human inner ear. Scientific data, 4(170132), p. 170132. Nature Publishing Group 10.1038/sdata.2017.132

Chandran, Vimal; Reyes, Mauricio; Zysset, Philippe (2017). A novel registration-based methodology for prediction of trabecular bone fabric from clinical QCT: A comprehensive analysis. PLoS ONE, 12(11), e0187874. Public Library of Science 10.1371/journal.pone.0187874

Porz, Nicole; Habegger, Simon; Meier, Raphael; Verma, Rajeev Kumar; Jilch, Astrid; Fichtner, Jens; Knecht, Urspeter; Radina, Christian; Schucht, Philippe; Beck, Jürgen; Raabe, Andreas; Slotboom, Johannes; Reyes, Mauricio; Wiest, Roland (2016). Fully Automated Enhanced Tumor Compartmentalization: Man vs. Machine Reloaded. PLoS ONE, 11(11), e0165302. Public Library of Science 10.1371/journal.pone.0165302

Correa Shokiche, Carlos Enrique; Baumann, Philipp; Hlushchuk, Ruslan; Djonov, Valentin; Reyes, Mauricio (17 October 2016). High-Throughput Glomeruli Analysis of micro-CT Kidney Images Using Tree Priors and Scalable Sparse Computation. In: International Conference on Medical Image Computing and Computer-Assisted Intervention. Lecture Notes in Computer Science: Vol. 9901 (pp. 370-378). Cham: Springer International Publishing 10.1007/978-3-319-46723-8_43

Maier, Oskar; Menze, Bjoern H; von der Gablentz, Janina; Häni, Levin; Heinrich, Mattias P; Liebrand, Matthias; Winzeck, Stefan; Basit, Abdul; Bentley, Paul; Chen, Liang; Christiaens, Daan; Dutil, Francis; Egger, Karl; Feng, Chaolu; Glocker, Ben; Götz, Michael; Haeck, Tom; Halme, Hanna-Leena; Havaei, Mohammad; Iftekharuddin, Khan M; ... (2016). ISLES 2015 - A public evaluation benchmark for ischemic stroke lesion segmentation from multispectral MRI. Medical image analysis, 35, pp. 250-269. Elsevier 10.1016/j.media.2016.07.009

Taghizadeh, Elham; Reyes, Mauricio (2016). Statistical Shape Model of the Leg to Improve the Treatment of Patella Pathology in Total Knee Arthroplasty. (Dissertation, University of Bern, Faculty of Mediciine)

Seif, Maryam; Mani, Laila-Yasmin; Lu, Huanxiang; Boesch, Christoph Hans; Reyes, Mauricio; Vogt, Bruno; Vermathen, Peter (2016). Diffusion tensor imaging of the human kidney: Does image registration permit scanning without respiratory triggering? Journal of magnetic resonance imaging, 44(2), n/a-n/a. Wiley Interscience 10.1002/jmri.25176

Taghizadeh, Elham; Reyes, Mauricio; Zysset, Philippe; Latypova, Adeliya; Terrier, Alexandre; Büchler, Philippe (2016). Biomechanical Role of Bone Anisotropy Estimated on Clinical CT Scans by Image Registration. Annals of biomedical engineering, 44(8), pp. 2505-2517. Springer 10.1007/s10439-016-1551-4

Taghizadeh, Elham; Kistler, Michael; Büchler, Philippe; Reyes, Mauricio (2016). Fast Prediction of Femoral Biomechanics Using Supervised Machine Learning and Statistical Shape Modeling. In: Joldes, Grand; Doyle, Barry; Wittek, Adam; Nielsen, Poul; Miller, Karol (eds.) Computational Biomechanics for Medicine X (pp. 115-127). Springer-Verlag New York

McKinley, Richard; Häni, Levin; Gralla, Jan; El-Koussy, Marwan; Bauer, S; Arnold, Marcel; Fischer, Urs; Jung, Simon; Mattmann, Kaspar; Reyes, Mauricio; Wiest, Roland (2016). Fully automated stroke tissue estimation using random forest classifiers (FASTER). Journal of cerebral blood flow and metabolism, 37(8), pp. 2728-2741. Nature Publishing Group 10.1177/0271678X16674221

Lu, Ping; Barazzetti, Livia; Chandran, Vimal; Gavaghan, Kate; Weber, Stefan; Gerber, Nicolas; Reyes, Mauricio (2016). Super-Resolution Classification Improves Facial Nerve Segmentation from CBCT Imaging. In: CURAC 2016 : 15. Jahrestagung der Deutschen Gesellschaft für Computer- und Roboterassistierte Chirurgie. 29.09.-01.10.2016.

Meier, Raphael; Karamitsou, Venetia; Habegger, Simon; Wiest, Roland; Reyes, Mauricio (2016). Parameter Learning for CRF-Based Tissue Segmentation of Brain Tumors. In: Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. Lecture Notes in Computer Science: Vol. 9556 (pp. 156-167). Cham: Springer International Publishing 10.1007/978-3-319-30858-6_14

Meier, Raphael; Knecht, Urspeter; Loosli, Tina; Bauer, Stefan; Slotboom, Johannes; Wiest, Roland; Reyes, Mauricio (2016). Clinical Evaluation of a Fully-automatic Segmentation Method for Longitudinal Brain Tumor Volumetry. Scientific Reports, 6(23376), p. 23376. Nature Publishing Group 10.1038/srep23376

Valenzuela, Waldo Enrique; Ferguson, Stephen John; Ignasiak, Dominika; Diserens, Gaëlle; Häni, Levin; Wiest, Roland; Vermathen, Peter; Boesch, Christoph Hans; Reyes, Mauricio (2016). FISICO: Fast Image SegmentatIon COrrection. PLoS ONE, 11(5), e0156035. Public Library of Science 10.1371/journal.pone.0156035

Taghizadeh, Elham; Reyes, Mauricio; Büchler, Philippe (2 October 2015). Statistical Model of Bone Mechanical Properties. In: Shape Symposium.

Cerrolaza, Juan J; Reyes, Mauricio; Summers, Ronald M; González-Ballester, Miguel Ángel; Linguraru, Marius George (2015). Automatic multi-resolution shape modeling of multi-organ structures. Medical image analysis, 25(1), pp. 11-21. Elsevier 10.1016/j.media.2015.04.003

Chandran, Vimal; Zysset, Philippe; Reyes, Mauricio (October 2015). Prediction of Trabecular Bone Anisotropy from Quantitative Computed Tomography using Supervised Learning and a Novel Morphometric Feature Descriptor. Medical Image Computing and Computer-Assisted Intervention - MICCAI 2015. 18th International Conference, Munich, Germany, October 5-9, 2015, Proceedings, Part I, 9349, pp. 621-628. Springer International Publishing 10.1007/978-3-319-24553-9_76

Chappuis, Vivianne; Engel, Odette; Shahim, Kamal; Reyes, Mauricio; Katsaros, Christos; Buser, Daniel (2015). Soft Tissue Alterations in Esthetic Postextraction Sites: A 3-Dimensional Analysis. Journal of dental research, 94(9), 187S-193S. Sage 10.1177/0022034515592869

Lu, Ping; Barazzetti, Livia; Chandran, Vimal; Gerber, Kate; Weber, Stefan; Gerber, Nicolas; Reyes, Mauricio (August 2015). Facial Nerve Image Enhancement from CBCT using Supervised Learning Technique. IEEE Engineering in Medicine and Biology Society conference proceedings, 2015, pp. 2964-2967. IEEE Service Center 10.1109/EMBC.2015.7319014

Seif, Maryam; Lu, Huanxiang; Boesch, Chris; Reyes, Mauricio; Vermathen, Peter (2015). Image registration for triggered and non-triggered DTI of the human kidney: Reduced variability of diffusion parameter estimation. Journal of magnetic resonance imaging, 41(5), pp. 1228-1235. Departments of Clinical Research and Radiology, University of Bern, Bern, Switzerland.: Wiley Interscience 10.1002/jmri.24671

Menze, Bjoern; Reyes, Mauricio; Van Leemput, Koen; Porz, Nicole; Wiest, Roland (2015). The Multimodal Brain TumorImage Segmentation Benchmark (BRATS). IEEE transactions on medical imaging, 34(10), pp. 199-2024. Institute of Electrical and Electronics Engineers IEEE 10.1109/TMI.2014.2377694

Taghizadeh, Elham; Latypova, Adeliya; Maquer, Ghislain Bernard; Reyes, Mauricio; Büchler, Philippe (2015). Including anisotropic information of trabecular bone using image registration. In: 21h Congress of the European Society of Biomechanics. Prague, Czech Republic. 05.-08.07.2015.

Rios Velazquez, Emmanuel; Meier, Raphael; Dunn, William D; Alexander, Brian; Wiest, Roland; Bauer, Stefan; Gutman, David A; Reyes, Mauricio; Aerts, Hugo J W L (2015). Fully automatic GBM segmentation in the TCGA-GBM dataset: Prognosis and correlation with VASARI features. Scientific Reports, 5(16822), p. 16822. Nature Publishing Group 10.1038/srep16822

Valenzuela, Waldo Enrique; Ferguson, Stephen J.; Ignasiak, Dominika; Diserens, Gaëlle; Vermathen, Peter; Boesch, Christoph Hans; Reyes, Mauricio (2015). Correction tool for Active Shape Model based lumbar muscle segmentation. IEEE Engineering in Medicine and Biology Society conference proceedings, pp. 3033-3036. IEEE Service Center 10.1109/EMBC.2015.7319031

Bonaretti, Serena; Seiler, Christof; Boichon, Christelle; Reyes, Mauricio; Büchler, Philippe (2014). Image-based vs. mesh-based statistical appearance models of the human femur: Implications for finite element simulations. Medical engineering & physics, 36(12), pp. 1626-1635. Elsevier 10.1016/j.medengphy.2014.09.006

Cerrolaza, Juan J.; Villanueva, Arantxa; Reyes, Mauricio; Cabeza, Rafael; González Ballester, Miguel Angel; Linguraru, Marius George (September 2014). Generalized Multiresolution Hierarchical Shape Models via Automatic Landmark Clusterization. In: Golland, Polina; Hata, Nobuhiko; Barillot, Christian; Hornegger, Joachim; Howe, Robert (eds.) Medical Image Computing and Computer-Assisted Intervention — MICCAI 2014. Proceedings, Part III. Boston, MA, USA. 14.09.-18.09.2014. 10.1007/978-3-319-10443-0_1

Gerig, Thomas; Shahim, Kamal; Reyes, Mauricio; Vetter, Thomas; Lüthi, Marcel (September 2014). Spatially Varying Registration using Gaussian Processes. In: Golland, Polina; Hata, Nobuhiko; Barillot, Christian; Hornegger, Joachim; Howe, Robert (eds.) Medical Image Computing and Computer-Assisted Intervention — MICCAI 2014. Proceedings, Part II. Lecture Notes in Computer Science: Vol. 8674 (pp. 413-420). Springer 10.1007/978-3-319-10470-6_52

Meier, Raphael; Bauer, Stefan; Slotboom, Johannes; Wiest, Roland; Reyes, Mauricio (September 2014). Patient-Specific Semi-Supervised Learning for Postoperative Brain Tumor Segmentation. In: Medical Image Computing and Computer-Assisted Intervention — MICCAI 2014. Proceedings, Part I. Lecture Notes in Computer Science: Vol. 17 (pp. 714-721). Springer

Seiler, Christof; Gazdhar, Amiq Ur Rahman; Reyes, Mauricio; Benneker, Lorin M; Geiser, Thomas; Siebenrock, Klaus A; Gantenbein-Ritter, Benjamin (2014). Time-lapse microscopy and classification of 2D human mesenchymal stem cells based on cell shape picks up myogenic from osteogenic and adipogenic differentiation. Journal of tissue engineering and regenerative medicine, 8(9), pp. 737-746. Chichester: John Wiley & Sons 10.1002/term.1575

Bauer, Stefan; Wiest, Roland; Slotboom, Johannes; Reyes, Mauricio (2014). Atlas-based Segmentation of Tumor-bearing Brain Images. In: Hayat, M.A. (ed.) Molecular Mechanisms, Children's Cancer, Treatments, and Radiosurgery. Tumors of the Central Nervous System: Vol. 12 (pp. 159-169). Dordrecht: Springer 10.1007/978-94-007-7217-5_14

Bauer, Stefan; Gratz, Pascal P.; Gralla, Jan; Reyes, Mauricio; Wiest, Roland (2014). Towards Automatic MRI Volumetry for Treatment Selection in Acute Ischemic Stroke Patients. In: Proceedings of the 36th Annual International Conference of the IEEE EMBS. Chicago, IL. 26.08.-30.08.2014. 10.1109/EMBC.2014.6943891

Taghizadeh, Elham; Maquer, Ghislain Bernard; Reyes, Mauricio; Büchler, Philippe (2014). Including the trabecular anisotropy from registered microCT data in homogenized FE model improves the bone's mechanical predictions (Unpublished). In: CMBBE 2014.

Bauer, Stefan; Porz, Nicole; Meier, Raphael; Pica, Alessia; Slotboom, Johannes; Wiest, Roland; Reyes, Mauricio (2014). Interactive Segmentation of MR Images from Brain Tumor Patients. In: ISBI 2014: Proceedings of the 2014 IEEE international conference on Biomedical imaging (pp. 862-865). Beijing: IEEE 10.1109/ISBI.2014.6868007

Chappuis, Vivianne; Engel, Odette; Reyes, Mauricio; Shahim, K; Nolte, L-P; Buser, Daniel (2013). Ridge alterations post-extraction in the esthetic zone: a 3D analysis with CBCT. Journal of dental research, 92(12 Sup), 195S-201S. Sage 10.1177/0022034513506713

Valenzuela, Waldo Enrique; Vermathen, Peter; Boesch, Christoph Hans; Nolte, Lutz-Peter; Reyes, Mauricio (1 October 2013). iSix - Image Segmentation in Osirix (Unpublished). In: 30th Annual Scientific Meeting of the European Society for Magnetic Resonance in Medicine and Biology. Toulouse, France. 03.10.-05.10.2013.

Shahim, Kamal; Jürgens, Philipp; Cattin, Philippe C.; Nolte, Lutz-P.; Reyes, Mauricio (October 2013). Prediction of Cranio-Maxilofacial Surgical Planning using an Inverse Soft Tissue Modelling Approach. In: The 16th Conference on Medical Image Computing and Computer Assisted Intervention — MICCAI 2013. Lecture Notes in Computer Science: Vol. 7908 (pp. 18-25). Springer 10.1007/978-3-642-40811-3_3

Jürgens, P.; Shahim, Kamal; Cattin, P.; Zeilhofer, H. F.; Reyes, Mauricio (October 2013). Backward-planning for orthognatic surgery - a new inverse modelling algorithm to define the hard-tissue position from a desired soft-tissue surface. International journal of oral & maxillofacial surgery, 42(10), p. 1331. Elsevier 10.1016/j.ijom.2013.07.557

Lu, Huanxiang; Beisteiner, Roland; Nolte, Lutz-Peter; Reyes, Mauricio (2013). Hierarchical segmentation-assisted multimodal registration for MR brain images. Computerized medical imaging and graphics, 37(3), pp. 234-244. Elsevier 10.1016/j.compmedimag.2013.03.004

Bauer, Stefan; Lu, Huanxiang; May, Christian P.; Nolte, Lutz-P.; Büchler, Philippe; Reyes, Mauricio (2013). Integrated Segmentation of Brain Tumor Images for Radiotherapy and Neurosurgery. International journal of imaging systems and technology, 23(1), pp. 59-63. John Wiley & Sons 10.1002/ima.22037

Bauer, Stefan; Fejes, Thomas; Reyes, Mauricio (2013). A Skull-Stripping Filter for ITK. Insight journal, 2012 Kitware, Inc.

Kim, Bo-Ram; Oh, Kyung-Min; Cevidanes, Lucia H.S.; Park, Jeong-Eon; Sim, Hyoung-Seob; Seo, Sung-Kyung; Reyes, Mauricio; Kim, Yoon-Ji; Park, Yang-Ho (2013). Analysis of 3D Soft Tissue Changes After 1- and 2-Jaw Orthognathic Surgery in Mandibular Prognathism Patients. Journal of oral and maxillofacial surgery, 71(1), pp. 151-161. Maryland Heights, Mo.: Elsevier 10.1016/j.joms.2012.02.005

Ritacco, Lucas Eduardo; Seiler, Christof; Farfalli, German Luis; Nolte, Lutz-Peter; Reyes, Mauricio; Muscolo, Domingo Luis; Tinao, Luis Aponte (2013). Validity of an automatic measure protocol in distal femur for allograft selection from a three-dimensional virtual bone bank system. Cell and Tissue Banking, 14(2), pp. 213-220. Springer 10.1007/s10561-012-9307-3

Bousleiman, Habib; Iizuka, Tateyuki; Nolte, Lutz-Peter; Reyes, Mauricio (2013). Population-based design of mandibular fixation plates with bone quality and morphology considerations. Annals of biomedical engineering, 41(2), pp. 377-384. Cambridge: Springer 10.1007/s10439-012-0671-8

Bousleiman, Habib; Paul, Laurent; Nolte, Lutz-Peter; Reyes, Mauricio (2013). Comparative Evaluation of Pelvic Allograft Selection Methods. Annals of biomedical engineering, 41(5), pp. 931-938. Springer 10.1007/s10439-013-0739-0

Shahim, Kamal; Goksel, O.; Jürgens, P.; Reyes, Mauricio (2013). Accuracy Improvement In Cranio-Maxillofacial Soft Tissue Simulation Using A Muscle Embedded Meshing Approach. IEEE Engineering in Medicine and Biology Society conference proceedings, 2013, pp. 7156-7159. IEEE Service Center 10.1109/EMBC.2013.6611208

Bauer, Stefan; Tessier, Jean; Krieter, Oliver; Nolte, Lutz-P.; Reyes, Mauricio (2013). Integrated Spatio-Temporal Segmentation of Longitudinal Brain Tumor Imaging Studies. In: Menze, Bjoern; Langs, Georg; Montillo, Albert; Kelm, Michael; Müller, Henning; Tu, Zhuowen (eds.) Medical Computer Vision. Large Data in Medical Imaging. Lecture Notes in Computer Science: Vol. 8331 (pp. 74-83). Springer International Publishing 10.1007/978-3-319-05530-5_8

Bauer, Stefan; Wiest, Roland; Nolte, Lutz-Peter; Reyes, Mauricio (2013). A survey of MRI-based medical image analysis for brain tumor studies. Physics in medicine and biology, 58(13), R97-R129. Bristol: Institute of Physics Publishing IOP 10.1088/0031-9155/58/13/R97

Oliveira-Santos, Thiago; Baumberger, Christian; Constantinescu, Mihai; Olariu, Radu; Nolte, Lutz-Peter; Alaraibi, Salman; Reyes, Mauricio (2013). 3D Face Reconstruction from 2D Pictures: First Results of a Web-Based Computer Aided System for Aesthetic Procedures. Annals of biomedical engineering, 41(5), pp. 952-966. Springer 10.1007/s10439-013-0744-3

Lüthi, Marcel; Blanc, Remi; Albrecht, Thomas; Gass, Tobias; Goksel, Orcun; Büchler, Philippe; Kistler, Michael; Bou Sleiman, Habib; Reyes, Mauricio; Cattin, Philippe; Vetter, Thomas (2012). Statismo - A framework for PCA based statistical models. Insight journal, p. 1. Clifton Park, NY: Kitware, Inc.

Lu, Huanxiang; Van der Zwaag, Wietske; Nolte, Lutz-Peter; Reyes, Mauricio (2012). Geometric and Intensity EPI Distortion Correction for 7T fMRI Using Simultaneous Classification and Registration. In: Proceedings of ESMRMB 2012. Lisbon, Portugal. 4-6 October 2012.

Seif, Maryam; Lu, Huanxiang; Boesch, Christoph Hans; Reyes, Mauricio; Vermathen, Peter (2012). Image co-registration for triggered and non-triggered DTI of the human kidney: Reduced variability of diffusion parameter estimation. In: Proceedings of ESMRMB 2012, Lisbon, Portugal.

Schulz, Arndt P.; Reimers, Nils; Wipf, Felix; Vallotton, Michel; Bonaretti, Serena; Kozic, Nina; Reyes, Mauricio; Kienast, Benjamin J. (2012). Evidence Based Development of a Novel Lateral Fibula Plate (VariAx Fibula) Using a Real CT Bone Data Based Optimization Process During Device Development. Open orthopaedics journal, 6(1), pp. 1-7. Sharjah: Bentham Open 10.2174/1874325001206010001

Lu, Huanxiang; Nolte, Lutz-Peter; Reyes, Mauricio (2012). Interest points localization for brain image using landmark-annotated atlas. International journal of imaging systems and technology, 22(2), p. 145. New York, N.Y.: John Wiley & Sons 10.1002/ima.22015

Bousleiman, Habib; Seiler, Christof; Iizuka, Tateyuki; Nolte, Lutz-Peter; Reyes, Mauricio (2012). Population-Based Design of Mandibular Plates Based on Bone Quality and Morphology. In: Ayache, Nicholas; Delingette, Hervé; Golland, Pollina; Mori, Kensaku (eds.) Medical Image Computing and Computer-Assisted Intervention – MICCAI 2012. Lecture notes in computer science: Vol. 15 (pp. 66-73). Berlin Heidelberg: Springer 10.1007/978-3-642-33415-3_9

Seiler, Christof; Pennec, Xavier; Reyes, Mauricio (2012). Simultaneous Multiscale Polyaffine Registration by Incorporating Deformation Statistics. In: Ayache, Nicholas; Delingette, Hervé; Golland, Polina (eds.) Medical Image Computing and Computer-Assisted Intervention – MICCAI 2012. Lecture Notes in Computer Science: Vol. 15 (pp. 130-137). Berlin Heidelberg: Springer 10.1007/978-3-642-33418-4_17

Blanc, Rémi; Seiler, Christof; Székely, Gabor; Nolte, Lutz-Peter; Reyes, Mauricio (2012). Statistical Model Based Shape Prediction from a Combination of Direct Observations and Various Surrogates. Application to Orthopaedic Research. Medical image analysis, 16(6), pp. 1156-1166. Amsterdam: Elsevier 10.1016/j.media.2012.04.004

Seiler, Christof; Pennec, Xavier; Nolte, Lutz-Peter; Reyes, Mauricio (2012). Capturing the Multiscale Anatomical Shape Variability with Polyaffine Transformation Trees. Medical image analysis, 16(7), pp. 1371-1384. Amsterdam: Elsevier 10.1016/j.media.2012.05.011

Gavaghan, K.; Oliveira-Santos, T.; Peterhans, M.; Reyes, Mauricio; Kim, H.; Anderegg, S.; Weber, S. (2012). Evaluation of a portable image overlay projector for the visualisation of surgical navigation data: phantom studies. International Journal of Computer Assisted Radiology and Surgery, 7(4), pp. 547-56. Berlin: Springer-Verlag 10.1007/s11548-011-0660-7

Bauer, Stefan; Ritacco, Lucas E.; Boesch, Chris; Nolte, Lutz-P.; Reyes, Mauricio (2012). Automatic Scan Planning for Magnetic Resonance Imaging of the Knee Joint. Annals of biomedical engineering, 40(9), pp. 2033-42. Cambridge: Springer 10.1007/s10439-012-0552-1

De Heras Ciechomski, Pablo; Constantinescu, Mihai; Garcia, Jaime; Olariu, Radu; Dindoyal, Irving; Le Huu, Serge; Reyes, Mauricio (2012). Development and implementation of a web-enabled 3D consultation tool for breast augmentation surgery based on 3D-image reconstruction of 2D pictures. Journal of medical internet research, 14(1), e21. Toronto: Centre of Global eHealth Innovation 10.2196/jmir.1903

Kim, Yoon-Ji; Oh, Kyung-Min; Hong, Ji-Suk; Lee, Jeong-Hwa; Kim, Hyung-Min; Reyes, Mauricio; Cevidanes, Lucia H.S.; Park, Yang-Ho (2011). Do Patients Treated With Bimaxillary Surgery Have More Stable Condylar Positions Than Those Who Have Undergone Single-Jaw Surgery? Journal of oral and maxillofacial surgery, 70(9), pp. 2143-2152. Elsevier 10.1016/j.joms.2011.08.028

Bonaretti, Serena; Seiler, Christof; Boichon, Christelle; Büchler, Philippe; Reyes, Mauricio (2011). Mesh-based vs. Image-based Statistical Appearance Model of the Human Femur: a Preliminary Comparison Study for the Creation of Finite Element Meshes. In: Proceedings of the MICCAI Workshop on Mesh Processing in Medical Image Analysis. Westin Harbor Castle, Toronto, Canada. 18.09.2011.

Kim, Hyung Min; Jürgens, Philipp; Reyes, Mauricio (2011). Soft-Tissue Simulation for Cranio-Maxillofacial Surgery: Clinical Needs and Technical Aspects. In: Gefen, Amit (ed.) Patient-Specific Modeling in Tomorrow's Medicine. Studies in Mechanobiology, Tissue Engineering and Biomaterials: Vol. 09 (pp. 413-440). Berlin-Heidelberg: Springer 10.1007/8415_2011_105

Seiler, Christof; Pennec, Xavier; Ritacco, Lucas; Reyes, Mauricio (2011). Femur Specific Polyaffine Model to Regularize the Log-Domain Demons Registration. In: 10th SPIE Medical Imaging 2010. 10.1117/12.878316

Bauer, Stefan; Nolte, Lutz-Peter; Reyes, Mauricio (2011). Fully Automatic Segmentation of Brain Tumor Images using Support Vector Machine Classiffication in Combination with Hierarchical Conditional Random Field Regularization. In: Fichtinger, Gabor; Martel, Anne; Peters, Terry (eds.) Medical Image Computing and Computer-Assisted Intervention – MICCAI 2011. 14th International Conferenc. Lecture Notes in Computer Science: Vol. 6893 (pp. 354-361). Berlin: Springer 10.1007/978-3-642-23626-6_44

Seiler, Christof; Pennec, Xavier; Reyes, Mauricio (2011). Geometry-Aware Multiscale Image Registration via OBBTree-Based Polyaffine Log-Demons. In: Gabor, Fichtinger; Martel, Anne; Peters, Terry (eds.) Medical Image Computing and Computer-Assisted Intervention – MICCAI 2011. 14th International Conference. Lecture Notes in Computer Science: Vol. 6892 (pp. 631-638). Berlin: Springer 10.1007/978-3-642-23629-7_77

Juergens, Philipp; Klug, Clemens; Krol, Zdzislaw; Beinemann, Jörg; Kim, Hyungmin; Reyes, Mauricio; Guevara-Rojas, Godoberto; Zeilhofer, Hans-Florian; Ewers, Rolf; Schicho, Kurt (2011). Navigation-Guided Harvesting of Autologous Iliac Crest Graft for Mandibular Reconstruction. Journal of oral and maxillofacial surgery, 69(11), pp. 2915-2923. Maryland Heights, Mo.: Elsevier 10.1016/j.joms.2010.12.045

Bauer, Stefan; Nolte, Lutz-Peter; Reyes, Mauricio (2011). Segmentation of brain tumor images based on atlas-registration combined with a Markov-Random-Field lesion growth model. In: ISBI'11: Proceedings of the 2011 IEEE international conference on Biomedical imaging (pp. 2018-2021). IEEE Press 10.1109/ISBI.2011.5872808

Lu, Huanxiang; Cattin, Philippe C.; Nolte, Lutz-Peter; Reyes, Mauricio (2011). Diffusion weighted imaging distortion correction using hybrid multimodal image registration. In: ISBI'11: Proceedings of the 2011 IEEE international conference on Biomedical imaging. IEEE International Symposium on Biomedical Imaging (pp. 594-597). IEEE Press 10.1109/ISBI.2011.5872477

Marias, Kostas; Dionysiou, Dimitra; Sakkalis, Vangelis; Graf, Norbert; Bohle, Rainer; Coveney, Peter; Wan, Shunzhou; Folarin, Amos; Büchler, Philippe; Reyes, Mauricio; Clapworthy, Gordon; Liu, Enjie; Sabczynski, J"org; Bily, Tomas; Roniotis, Alexandros; Tsiknakis, Manolis; Kolokotroni, Eleni; Giatili, Stavroula; Veith, Christian; Messe, E.; ... (2011). Clinically driven design of multi-scale cancer models : the ContraCancrum project paradigm. Interface - journal of the Royal Society, 1(3), pp. 450-461. London: The Royal Society 10.1098/rsfs.2010.0037

Peterhans, Matthias; Frei, Daniel; Manser, Peter; Reyes, Mauricio; Fix, Michael K (2011). Monte Carlo Dose Calculation on Deforming Anatomy. Zeitschrift für medizinische Physik, 21(2), pp. 113-23. Amsterdam: Elsevier, Urban & Fischer 10.1016/j.zemedi.2010.11.002

Jürgens, P.; Kim, H.; Forter, S.; Beinemann, J.; Zeilhofer, H.F.; Reyes, Mauricio; Schwenzer, K. (2011). Three-dimensional control of maxillary position--validation of a 3-d real time navigational prototype system for routine application in orthognathic surgery. International journal of oral & maxillofacial surgery, 40(10), p. 1064. Elsevier 10.1016/j.ijom.2011.07.131

Jürgens, P.; Kim, H.; Reyes, Mauricio (2011). Application of a new soft-tissue simulation strategy based on a mimic muscle template model to predict the outcome in orthognatic surgery. International journal of oral & maxillofacial surgery, 40(10), p. 1064. Elsevier 10.1016/j.ijom.2011.07.130

Bou Sleiman, Habib; Ritacco, Lucas; Nolte, Lutz-Peter; Reyes, Mauricio (2011). Minimization of Intra-Operative Shaping of Orthopaedic Fixation Plates: A Population-Based Design. In: Fichtinger, Gabor; Martel, Anne; Peters, Terry (eds.) Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2011. Lecture Notes in Computer Science: Vol. 14 (pp. 409-416). Berlin Heidelberg: Springer 10.1007/978-3-642-23629-7_50

Bauer, Stefan; May, Christian; Dionysiou, Dimitra; Stamatakos, Georgios; Büchler, Philippe; Reyes, Mauricio (2011). Multi-Scale Modeling for Image Analysis of Brain Tumor Studies. IEEE transactions on biomedical engineering, 59(1), pp. 25-29. New York, N.Y.: Institute of Electrical and Electronics Engineers IEEE 10.1109/TBME.2011.2163406

Bou Sleiman, Habib; Ritacco, Lucas E.; Aponte-Tinao, Luis; Muscolo, Domingo L.; Nolte, Lutz-Peter; Reyes, Mauricio (2011). Allograft Selection for Transepiphyseal Tumor Resection Around the Knee Using Three-Dimensional Surface Registration. Annals of biomedical engineering, 39(6), pp. 1720-1727. Cambridge: Springer US; http://www.springer-ny.com 10.1007/s10439-011-0282-9

Seiler, C.; Gazdhar, A.; Geiser, T.; Reyes, Mauricio; Gantenbein-Ritter, Benjamin (June 2010). Mesenchymal Stem Cell Classification during Differentiation Based on Shape Information (Unpublished). In: TERMIS -- Tissue Engineering and Regenerative Medicine International Society.

Lu, Huanxiang; Reyes, Mauricio; Šerifović, Amira; Weber, Stefan; Sakurai, Yasuo; Yamagata, Hitoshi; Cattin, Philippe C. (April 2010). Multi-modal diffeomorphic demons registration based on point-wise mutual information. In: ISBI'10: Proceedings of the 2010 IEEE international conference on Biomedical imaging (pp. 372-375). IEEE 10.1109/ISBI.2010.5490333

Lu, Huanxiang; Cattin, Philippe C; Reyes, Mauricio (2010). A Hybrid Multimodal Non-Rigid Registration of MR Images Based on Diffeomorphic Demons. In: 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) 2010 (pp. 5951-5954). IEEE 10.1109/IEMBS.2010.5627562

Bauer, Stefan; Seiler, Christof; Bardyn, Thibaut; Buechler, Philippe; Reyes, Mauricio (2010). Atlas-Based Segmentation of Brain Tumor Images Using a Markov Random Field-Based Tumor Growth Model and Non-Rigid Registration. In: 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) 2010 (pp. 4080-4083). IEEE 10.1109/IEMBS.2010.5627302

Bonaretti, Serena; Reyes, Mauricio; Kistler, Michael; Seiler, Christof; Büchler, Philippe (2010). Combined statistical model of bone shape and mechanical properties for bone and implant modeling (Unpublished). In: 9th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering, Valencia/Spain, Feb 24-27.

Bou Sleiman, Habib; Ritacco, Lucas E.; Reyes, Mauricio (2010). Computer-assisted allograft selection for transepiphyseal tumor resection at the knee (Unpublished). In: 10th Annual Meeting of the International Society for Computer Assisted Surgery, Paris, France, June 16-19.

Kim, H; Jürgens, P; Cattin, P; Weber, S; Nolte, L.P; Reyes, Mauricio (2010). Fast soft-tissue simulation method for cranio-maxillofacial surgery using facial muscle template models (Unpublished). In: 14th Annual Conference of the International Society for Computer Aided Surgery, Geneva, Switzerland, June.

Reyes, Mauricio; González Ballester, Miguel A.; Kozic, Nina; Summers, Ronald M.; Linguraru, Marius G. (2010). Hierarchical Patch Generation for Multi-level Statistical Shape Analysis by Principal Factor Analysis Decomposition. In: 9th SPIE Medical Imaging 2010. Biomedical Applications in Molecular, Structural, and Functional Imaging. 10.1117/12.843253

Kim, H; Jürgens, P; Cattin, P; Weber, S; Nolte, LP; Reyes, Mauricio (2010). Patient-specific, Fast Soft-Tissue Simulation for Cranio-Maxillofacial Surgery (Unpublished). In: 17th Congress of the European Society of Biomechanics. Edinburgh, U.K..

Cevidanes, L; Tucker, S; Styner, M; Kim, Hyungmin; Chapuis, J; Reyes, Mauricio; Proffit, W; Turvey, T; Jaskolka, M (2010). Three-dimensional surgical simulation. American journal of orthodontics and dentofacial orthopedics, 138(3), 361 - 371. St. Louis, Mo.: Mosby 10.1016/j.ajodo.2009.08.026

Kim, Hyungmin; Jürgens, Philipp; Weber, Stefan; Nolte, Lutz-Peter; Reyes, Mauricio (2010). A New Soft-Tissue Simulation Strategy for Cranio-Maxillofacial Surgery Using Facial Muscle Template Model. Progress in biophysics and molecular biology, 103(2-3), pp. 284-291. Kidlington, UK: Elsevier Science 10.1016/j.pbiomolbio.2010.09.004

Tucker, S; Cevidanes, L; Styner, M; Kim, H; Reyes, Mauricio; Proffit, W; Turvey, T (2010). Comparison of actual surgical outcomes and 3-dimensional surgical simulations. Journal of oral and maxillofacial surgery, 68(10), pp. 2412-2421. Maryland Heights, Mo.: Elsevier 10.1016/j.joms.2009.09.058

Kim, Hyung Min; Jürgens, Philipp; Nolte, Lutz-Peter; Reyes, Mauricio (2010). Anatomically-Driven Soft-Tissue Simulation Strategy for Cranio-Maxillofacial Surgery Using Facial Muscle Template Model. In: Jiang, Tianzi; Navab, Nassir; Pluim, Josien; Viergever, Max (eds.) Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2010. Lecture Notes in Computer Science: Vol. 6361 (pp. 61-68). Heidelberg: Springer 10.1007/978-3-642-15705-9_8

Seiler, Christof; Gazdhar, A; Geiser, T; Reyes, Mauricio; Gantenbein-Ritter, Benjamin (2010). Mesenchymal Stem Cell Classification during Differentiation Based on Shape Information (Unpublished).

Seiler, Christof; Pennec, Xavier; Reyes, Mauricio (2010). Parametric regression of 3D medical images through the exploration of non-parametric regression models. In: ISBI'10: Proceedings of the 2010 IEEE international conference on Biomedical imaging (pp. 452-455). IEEE Press 10.1109/ISBI.2010.5490313

Kozic, Nina; Weber, Stefan; Büchler, Philippe; Lutz, Christian; Reimers, Nils; González Ballester, Miguel A.; Reyes, Mauricio (2010). Optimisation of orthopaedic implant design using statistical shape space analysis based on level sets. Medical image analysis, 14(3), pp. 265-275. Amsterdam: Elsevier 10.1016/j.media.2010.02.008

May, Christian; Bardyn, Thibaut; Reyes, Mauricio; Büchler, Philippe (2010). Biomechanical model of tumor growth: application to the European ContraCancrum project. In: Stamatakos, G.; Dionysiou, D. (eds.) Proceedings of the 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation The ContraCancrum Workshop.

Bonaretti, Serena; Helgason, Benedikt; Seiler, Christof; Kistler, Michael; Reyes, Mauricio; Büchler, Philippe (2010). A statistical shape model of bone anatomical variability for finite element assessment of bone mechanics. In: Proceedings of the 17th Congress of the European Society of Biomechanics. University of Edinburgh, UK. 5-8 July 2010.

Oliveira Dos Santos, Thiago; Peterhans, Matthias; Roth, Beat; Thalmann, George; Reyes, Mauricio; Nolte, Lutz-Peter; Weber, Stefan (2010). Computer Aided Surgery for Percutaneous Nephrolithotomy: Clinical Requirement Analysis and System Design. In: Proceedings of IEEE Engineering in Medicine and Biology Society Conference EMBC. Buenos Aires, Argentina. 31.08.-04.09.2010. 10.1109/IEMBS.2010.5627387

Dong, Xiao; Lu, Huanxiang; Sakurai, Yasuo; Yamagata, Hitoshi; Zheng, Guoyan; Reyes, Mauricio (2010). Automated Intervertebral Disc Detection from Low Resolution, Sparse MRI Images for the Planning of Scan Geometries. In: Wang, Fei; Yan, Pingkun; Suzuki, Kenji; Shen, Dinggang (eds.) Machine learning in Medical Imaging (MLMI) - MICCAI 2010 Workshop. Lecture Notes in Computer Science: Vol. 6357 (pp. 10-17). Berlin: Springer 10.1007/978-3-642-15948-0_2

Bardyn, Thibaut; Reyes, Mauricio; Larrea, Xabier; Büchler, Philippe (2010). Influence of Smoothing on Voxel-Based Mesh Accuracy in Micro-Finite Element. In: Miller, Karol; Nielsen, Pourl M F (eds.) Computational Biomechanics for Medicine (pp. 85-93). New York: Springer 10.1007/978-1-4419-5874-7_10

Stamatakos, G.; Dionysiou, D.; Kolokotroni, E.; Georgiadi, E.; Roniotis, A.; Sakkalis, V.; Coveney, P.; Wan, S.; Manos, S.; Zasada, S.; Folarin, A.; Büchler, P.; Bardyn, T.; Bauer, S.; Reyes, Mauricio; Bily, T.; Bednar, V.; Karasek., M.; Graf, N.; Bohle, R.M.; ... (2010). CONTRA CANCRUM AT THE PROJECT LEVEL: The ContraCancrum Oncosimulator: Integrating Biomechanisms Across Scales in the Clinical Context. In: Stamatakos, G.; Dionysiou, D. (eds.) Proceedings of the 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation. Athens, Greece. 08.09.-09.09.2010.

Marias, K.; Sakkalis, V.; Roniotis, A.; Karatzanis, I.; Stamatakos, G.; Dionysiou, D.; Giatili, S.; Uzunoglou, N.; Graf, N.; Bohle, R.; Meese, E.; Stenzhorn, H.; Kim, Y.-J.; Coveney, P.; Zasada, S.; Wan, S.; Folarin, A.; Büchler, P.; Bardyn, T.; Bauer, S.; ... (2010). Clinically Oriented Translational Cancer Multilevel Modelling: The ContraCancrum project (Unpublished). In: Proceedings of the Virtual Physiological Human Conference 2010.

Marias, K.; Sakkalis, V.; Roniotis, A.; Karatzanis, I.; Stamatakos, G.; Dionysiou, D.; Giatili, S.; Uzunoglou, N.; Graf, N.; Bohle, R.; Meese, E.; Stenzhorn, H.; Kim, Y.-J.; Coveney, P.; Zasada, S.; Wan, S.; Folarin, A.; Büchler, P.; Bardyn, T.; Bauer, S.; ... (2010). CONTRACANCRUM AT THE PROJECT LEVEL: Clinically Oriented Translational Cancer Multilevel Modelling. In: Stamatakos, G.; Dionysiou, D. (eds.) Proceedings of the 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation. Athens, Greece. 08.09.-09.09.2010.

Bauer, Stefan; Reyes, Mauricio (2010). A Markov-Random-Field-Based Biomechanical Tumor Growth Model for Atlas-Based Segmentation of Brain Tumor Images. In: Proceedings of the 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation.

Kozic, Nina; Weber, Stefan; González-Ballester, Miguel A.; Abdo, G; Rufenacht, DA; Ferguson, Stephen J.; Reyes, Mauricio (2010). Automated cement segmentation in vertebroplasty. Computer aided surgery, 15(1-3), pp. 49-55. Abingdon, UK: Taylor & Francis 10.3109/10929088.2010.496176

Oliveira-Santos, Thiago; Weitzel, Thilo; Klaeser, Bernd; Krause, Thomas; Nolte, Lutz-Peter; Weber, Stefan; Reyes, Mauricio (2010). Multimodal target correction by local bone registration: a PET/CT evaluation. IEEE Engineering in Medicine and Biology Society conference proceedings, 2010, pp. 5616-5619. Piscataway, N.J.: IEEE Service Center 10.1109/IEMBS.2010.5626797

Kim, Hyungmin; Jürgens, Philipp; Nolte, Lutz P.; Weber, Stefan; Zeilhofer, Hans-Florian; Reyes, Mauricio (2009). Anatomically considered, fast soft-tissue simulation for cranio-maxillofacial surgery (Unpublished). In: Computer Aided Surgery around the Head.

Reyes, Mauricio; González-Ballester, Miguel A.; Li, Zhixi; Kozic, Nina; Chin, See; Summers, Ronald M.; Linguraru, Marius George (2009). Anatomical variability of organs via principal factor analysis from the construction of an abdominal probabilistic atlas. In: IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2009. ISBI '09. Boston, MA. 28.06.-01.07.2009. 10.1109/ISBI.2009.5193139

Bardyn, T.; Reyes, Mauricio; Boyd, S.; Büchler, Philippe (2009). Influence of smoothing on voxel-based mesh accuracy in micro finite-element.

Blanc, Remi; Reyes, Mauricio; Seiler, Christof; Székely, Gabor (2009). Conditional variability of statistical shape models based on surrogate variables. In: Medical Image Computing and Computer-Assisted Intervention MICCAI 2009. Lecture Notes in Computer Science (pp. 84-91). Springer

Seiler, Christof; Weber, Stefan; Schmidt, Walter; Fischer, Felix; Reimers, Nils; Reyes, Mauricio (2009). Automatic landmark propagation for left and right symmetry assessment of tibia and femur: A computational anatomy based approach. In: 9th Annual Meeting of the International Society for Computer Assisted Surgery.

Bonaretti, Serena; Büchler, Philippe; Reimers, Nils; Schmidt, Walter; Seiler, Christof; Weber, Stefan; Reyes, Mauricio (2009). Automatic bone density evaluation from CT images. In: 9th Annual Meeting of the International Society for Computer Assisted Orthopaedic Surgery. Boston, MA, USA. 17.06.-20.06.2009.

Schmidt, Walter; Reyes, Mauricio; Fischer, Felix; Geesink, Ruud; Nolte, Lutz; Racanelli, Joseph; Reimers, Nils (2009). Quantifying human knee anthropometric differences between ethnic groups and gender using shape analysis. In: Annual Meeting of the American Society of Biomechanics.

Bardyn, T; Reyes, M; Boyd, S; Büchler, P (2009). Automatic Finite Element Mesh Generation and Correction from 3D Image Data. In: IFMBE Proceedings.

Marias, K; Sakkalis, V; Roniotis, A; Farmaki, C; Stamatakos, G; Dionysiou, D; Giatili, S; Uzunoglou, N; Graf, N; Bohle, R; Messe, E; Coveney, PV; Manos, S; Wan, S; Folarin, A; Nagl, S; Büchler, Philippe; Bardyn, T; Reyes, M; Clapworthy, G; ... (2009). Clinically Oriented Translational Cancer Multilevel Modeling: The ContraCancrum Project. In: IFMBE Proceedings.

Seiler, Christof; Büchler, Philippe; Nolte, Lutz-Peter; Reyes, Mauricio; Paulsen, Rasmus (2009). Hierarchical Markov Random Fields Applied to Model Soft Tissue Deformations on Graphics Hardware. In: Magnenat-Thalmann, Nadia; Zhang, Jian J; Feng, David D (eds.) Recent Advances in the 3D Physiological Human (pp. 133-148). Heidelberg: Springer Verlag 10.1007/978-1-84882-565-9_9

Santos, TO; Weitzel, T; Klaeser, B; Reyes, Mauricio; Weber, Stefan (2009). Introducing computer-assisted surgery into combined PET/CT based biopsy treatments. In: 9th Annual Meeting of the International Society for Computer Assisted Orthopaedic Surgery. Boston, MA. 17.06.-20.06.2009.

Kozic, Nina; González-Ballester, Miguel A.; Büchler, Philippe; Reimers, Nils; Nolte, Lutz P.; Linguraru, Marius G.; Reyes, Mauricio (2009). Population-specific evaluation of implant bone fitting using PCA shape space and level sets. In: International Symposium on Biomedical Imaging: From Nano to Macro, 2009. ISBI '09. Boston, MA. 28.06.-01.07.2009. 10.1109/ISBI.2009.5193194

Kozic, Nina; Reyes, Mauricio; Tannast, Moritz; Nolte, Lutz-Peter; Gonzalez Ballester, Miguel A. (June 2008). Assesment of anatomical criteria across populations using statistical shape models and level sets. In: 8th Annual Meeting of the International Society for Computer Assisted Orthopaedic Surgery.

Kozic, N; Reyes, M; Nolte, L.P.; Ballester, M.A.Gonzalez (2008). Global Optimisation in PCA Shape Space Using Level Sets. In: 12th Annual Conference of the International Society for Computer Aided Surgery. Barcelona, Spain.

Reyes, Mauricio; Gonzalez Ballester, Miguel A.; Li, Zhixi; Kozic, Nina; Summers, Ronald M.; Linguraru, Marius George (2008). Interpretability of anatomical variability analysis of abdominal organs via clusterization of decomposition modes. In: Proceedings of the 30th Annual International Conference of the IEEE EMBS Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society Conference Proceedings (pp. 355-358). IEEE 10.1109/IEMBS.2008.4649163

Reyes, Mauricio; Bonaretti, Serena; Reimers, Nils; Lutz, Christian; Gonzalez Ballester, Miguel A. (2008). Evidence-based implant design using statistical bone model and automated implant fitting. In: Proceedings of Computer Assisted Orthopaedic Surgery International. 8th Annual Meeting. Hong Kong, China. 04.06.-07.06.2008.

Linguraru, M.G.; Vercauteren, T; Reyes, M; Ballester, M.A.Gonzalez; Ayache, N (2008). Segmentation Propagation from Deformable Atlases for Brain Mapping and Analysis. In: Proceedings of Brain Mapping Research Trends. New York, NY.

Bonaretti, S; Reimers, Nils; Rueckert, Daniel; Reyes, Mauricio; Gonzàlez, Miguel; Büchler, Philippe (2008). Statistical finite element analysis for bone modeling. Journal of biomechanics, 41(S1), S369-S369. Elsevier

Reyes, Mauricio; Larrea, Xabier; Boyd, Steven; Gonzalez Ballester, M.A.; Büchler, Philippe (2008). Constrained hexahedral mesh smoothing for finite element modelling from 3D image datag (Unpublished). In: Proceedings of the 8th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering.

Larrea, Xabier; Reyes, Mauricio; Boyd, S; Büchler, Philippe; Gonzales, M.A. (2008). Automatic Mesh Smoothing For Finite Element Modeling From 3d Image Data. In: Journal of Biomechanics.

Kozic, Nina; Reyes, Mauricio; Tannast, M; Nolte, Lutz-Peter; Ballester, MA Gonzalez (2008). Assessment of anatomical criteria across populations using statistical shape models and level sets. In: Proceedings of Computer Assisted Orthopaedic Surgery International.

Bonaretti, Serena; Reimers, Nils; Reyes, Mauricio; Nikitsin, Andrei; Joensson, Anders; Nolte, Lutz-Peter; Büchler, Philippe (2008). Assessment of Peri-Articular Implant Fitting Based on Statistical Finite Element Modeling. In: Proceedings of MICCAI Workshop - Computational Biomechanics for Medicine.

Reyes, Mauricio; Linguraru, M; Nolte, LP; Ballester, MA Gonzalez (2008). Clusterization of deformation modes for quantitative evaluation on factor analysis techniques on statistical shape modelling. In: Proceedings of Medical Imaging and Augmented Reality. Tokyo, Japan.

Larrea, Xabier; Reyes, Mauricio; Boyd, Stephen; Büchler, Philippe; Gonzalez, Miguel A. (2008). Automatic mesh smoothing for finite element modelling from 3D image data. (Unpublished). In: 16th Congress of the European Society of Biomechanics.

Kozic, Nina; Gonzalez Ballester, Miguel A.; Tannast, Moritz; Nolte, Lutz P.; Reyes, Mauricio (2008). Statistical Shape Space Analysis Based on Level Sets. In: Dohi, Takeyoshi; Sakuma, Ichiro; Liao, Hongen (eds.) Proceedings of Medical Imaging and Augmented Reality. Tokyo, Japan. 01.08.-02.08.2008. 10.1007/978-3-540-79982-5_18

Reyes, Mauricio A.; Gonzalez Ballester, Miguel A. (June 2007). Clustering of deformation modes for quantitative evaluation of statistical shape models. In: 7th Annual Meeting of the International Society for Computer Assisted Orthopaedic Surgery. Heidelberg, Germany. 20.06.-23.06.2007.

Reyes, Mauricio; Malandain, G; Koulibaly, PM; Gonzalez Ballester, MA; Darcourt, J (2007). Model-based respiratory motion compensation for emission tomography image reconstruction. Physics in medicine and biology, 52(12), pp. 3579-3600. Bristol: Institute of Physics Publishing IOP 10.1088/0031-9155/52/12/016

Reyes, Mauricio; Linguraru, Marius George; Marias, Kostas; Ayache, Nicholas; Nolte, Lutz-Peter; Gonzalez Ballester, Miguel Angel (2007). Statistical shape analysis via principal factor analysis. In: 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2007. ISBI 2007 (pp. 1216-1219). Washington DC, USA: IEEE 10.1109/ISBI.2007.357077

Linguraru, Marius George; Vercauteren, Tom; Reyes, Mauricio; González-Ballester, Miguel Ángel; Ayache, Nicholas (2007). Segmentation propagation from deformable atlases for brain mapping and analysis. Brain Research Journal, 1(4), pp. 269-287. Nova Science Publishers

Reyes, Mauricio; González-Ballester, M.A.; Linguraru, M.G. (2007). Statistical Bone Shape Analysis for Image Free Surgery. Acta Universitatis Cibiniensis, Technical Series, LV, pp. 121-129. De Gruyter

Malandain, G.; Reyes, Mauricio (December 2005). La tomographie en mouvement. Pour la science, 338, pp. 132-137.

Reyes, Mauricio; Malandain, Grégoire; Koulibaly, Pierre Malick; Darcourt, Jacques (July 2005). Respiratory motion correction in emission tomography imaging. In: Fully Three-Dimensional Image Reconstruction Meeting in Radiology and Nuclear Medicine. Salt Lake City, Utah, USA.

Reyes, Mauricio (2005). Respiratory Motion Compensation in Emission Tomography (Unpublished). (Dissertation, University of Nice, Sophia Antipolis, France)

Reyes, Mauricio; Malandain, Grégoire; Koulibaly, Pierre Malick; Gonzalez Ballester, Miguel A.; Darcourt, Jacques (2005). Respiratory motion correction in emission tomography image reconstruction. In: Duncan, J.; Gerig, G. (eds.) Medical Image Computing and Computer-Assisted Intervention — MICCAI 2005. Lecture Notes in Computer Science: Vol. 3750 (pp. 369-376). Verlag: Springer

Gonzalez Ballester, Miguel Angel; Linguraru, Marius George; Reyes, Mauricio; Ayache, Nicholas (2005). On the adequacy of principal factor analysis for the study of shape variability. In: Fitzpatrick, J. Michael; Reinhardt, Joseph M. (eds.) SPIE Medical Imaging 2005: Image Processing. Proceeding SPIE: Vol. 5747 (p. 1392). SPIE Publishing 10.1117/12.593333

Reyes, Mauricio; Malandain, G.; Ayache, N.; Darcourt, J.; Koulibaly, P.M. (2005). Respiratory motion compensation within emission tomographic reconstruction (Unpublished). In: 52nd Annual Meeting of the Society of Nuclear Medicine. Toronto, Canada.

Reyes, Mauricio; Malandain, Grégoire; Darcourt, Jacques (2004). Respiratory movement correction in emission tomography (Thème BIO 5279). Le Chesnay Cedex: Inria Sophia Antipolis