Publications
2026
++nnU-Net: Scaling nnU-Net with Prefix-Based Data Augmentation
Ana Sofia Ferreira Santos, André Ferreira, Gijs Luijten, Naida Solak, Lisle Faray de Paiva, Behrus Hinrichs-Puladi, Jens Kleesiek, Jan Egger, Victor Alves
arXiv
Achieving Over 10× Faster Sample Generation with Conditional Denoising Diffusion
André Ferreira, Gijs Luijten, Behrus Hinrichs-Puladi, Jens Kleesiek, Victor Alves, Jan Egger
Segmentation, Classification, and Synthesis for Brain Tumors and Traumatic Brain Injuries 2025
MedShapeNet -- A Large-Scale Dataset of 3D Medical Shapes for Computer Vision
Jianning Li, Antonio Pepe, Christina Gsaxner, Gijs Luijten, Yuan Jin, Narmada Ambigapathy, Enrico Nasca, Naida Solak, Gian Marco Melito, Afaque Rafique Memon, Xiaojun Chen, Jan Stefan Kirschke, Ezequiel de la Rosa, Patrick Ferdinand Christ, Hongwei Bran Li, David G. Ellis, Michele R. Aizenberg, Sergios Gatidis, Thomas Kuestner, Nadya Shusharina, Nicholas Heller, Vincent Andrearczyk, Adrien Depeursinge, Mathieu Hatt, Anjany Sekuboyina, Maximilian Loeffler, Hans Liebl, Reuben Dorent, Tom Vercauteren, Jonathan Shapey, Aaron Kujawa, Stefan Cornelissen, Patrick Langenhuizen, Achraf Ben-Hamadou, Ahmed Rekik, Sergi Pujades, Edmond Boyer, Federico Bolelli, Costantino Grana, Luca Lumetti, Hamidreza Salehi, Jun Ma, Yao Zhang, Ramtin Gharleghi, Susann Beier, Eduardo A. Garza-Villarreal, Thania Balducci, Diego Angeles-Valdez, Roberto Souza, Leticia Rittner, Richard Frayne, Yuanfeng Ji, Soumick Chatterjee, Andreas Nuernberger, Joao Pedrosa, Carlos Ferreira, Guilherme Aresta, Antonio Cunha, Aurelio Campilho, Yannick Suter, Jose Garcia, Alain Lalande, Emmanuel Audenaert, Claudia Krebs, Timo Van Leeuwen, Evie Vereecke, Rainer Roehrig, Frank Hoelzle, Vahid Badeli, Kathrin Krieger, Matthias Gunzer, Jianxu Chen, Amin Dada, Miriam Balzer, Jana Fragemann, Frederic Jonske, Moritz Rempe, Stanislav Malorodov, Fin Hendrik Bahnsen, Constantin Seibold, Alexander Jaus, Ana Sofia Ferreira Santos, Mariana Lindo, André Ferreira, Victor Alves, Michael Kamp, Amr Abourayya, Felix Nensa, Fabian Hoerst, Alexander Brehmer, Lukas Heine, Lars E. Podleska, Matthias A. Fink, Julius Keyl, Konstantinos Tserpes, Moon-Sung Kim, Shireen Elhabian, Hans Lamecker, Dzenan Zukic, Beatriz Paniagua, Christian Wachinger, Martin Urschler, Luc Duong, Jakob Wasserthal, Peter F. Hoyer, Oliver Basu, Thomas Maal, Max J. H. Witjes, Ping Luo, Björn Menze, Mauricio Reyes, Christos Davatzikos, Behrus Puladi, Jens Kleesiek, Jan Egger, Zongwei Zhou, Jiancheng Yang, Chongyu Qu, Tiezheng Zhang, Xiaoxi Chen, Wenxuan Li, Marek Wodzinski, Paul Friedrich, Kangxian Xie, Viet Duc Vu, Christopher Schlachta, Sandrine De Ribaupierre, Rajnikant Patel, Roy Eagleson, Heinrich Mächler, Thomas Küstner, Arcot Sowmya, Vincenzo Ferrari, Florian Dubost, Stefanie Schreiber, Hendrik Mattern, Oliver Speck, Daniel Haehn, Christoph John, Vicky Vandenbossche, Aline Van Oevelen, Kate Duquesne, Hamza Mekhzoum, Jef Vandemeulebroucke, Hauke Heidemeyer, Rainer Röhrig, Frank Hölzle, Timo van Meegdenburg, Zdravko Marinov, Paul F. Jäger, Rainer Stiefelhagen, Fabian Hörst, Yannik Hanusrichter, Martin Weßling, Marcel Dudda, Gregor Schiele, Ti-chiun Chang, Seyed-Ahmad Ahmadi, Thomas M. Deserno, Pascal Fua, Alan L. Yuille
Biomedical Engineering / Biomedizinische Technik
Comparative Analysis of nnUNet and MedNeXt for Head and Neck Tumor Segmentation in MRI-Guided Radiotherapy
Nikoo Moradi, André Ferreira, Behrus Puladi, Jens Kleesiek, Emad Fatemizadeh, Gijs Luijten, Victor Alves, Jan Egger
Head and Neck Tumor Segmentation for MR-Guided Applications 2024
Brain Tumour Removing and Missing Modality Generation using 3D WDM
André Ferreira, Gijs Luijten, Behrus Puladi, Jens Kleesiek, Victor Alves, Jan Egger
arXiv
Improved Multi-Task Brain Tumour Segmentation with Synthetic Data Augmentation
André Ferreira, Tiago Jesus, Behrus Puladi, Jens Kleesiek, Victor Alves, Jan Egger
arXiv
How we won BraTS 2023 Adult Glioma challenge? Just faking it! Enhanced Synthetic Data Augmentation and Model Ensemble for brain tumour segmentation
André Ferreira, Naida Solak, Jianning Li, Philipp Dammann, Jens Kleesiek, Victor Alves, Jan Egger
arXiv
GAN-based generation of realistic 3D volumetric data: A systematic review and taxonomy
André Ferreira, Jianning Li, Kelsey L. Pomykala, Jens Kleesiek, Victor Alves, Jan Egger
Medical Image Analysis
Deep PCCT: Photon Counting Computed Tomography Deep Learning Applications Review
Ana Carolina Alves, André Ferreira, Gijs Luijten, Jens Kleesiek, Behrus Puladi, Jan Egger, Victor Alves
arXiv
Multilingual Natural Language Processing Model for Radiology Reports -- The Summary is all you need!
Mariana Lindo, Ana Sofia Ferreira Santos, André Ferreira, Jianning Li, Gijs Luijten, Gustavo Correia, Moon-Sung Kim, Benedikt Michael Schaarschmidt, Cornelius Deuschl, Johannes Haubold, Jens Kleesiek, Jan Egger, Victor Alves
arXiv 2022
Open-Source Skull Reconstruction with MONAI
Jianning Li, André Ferreira, Behrus Puladi, Victor Alves, Michael Kamp, Moon-Sung Kim, Felix Nensa, Jens Kleesiek, Seyed-Ahmad Ahmadi, Jan Egger
arXiv
AutoPET Challenge: Combining nn-Unet with Swin UNETR Augmented by Maximum Intensity Projection Classifier
Lars Heiliger, Zdravko Marinov, André Ferreira, Jana Fragemann, Jacob M. Murray, David Kersting, Rainer Stiefelhagen, Jens Kleesiek
arXiv
GAN-based generation of realistic 3D data: A systematic review and taxonomy
André Ferreira, Jianning Li, Kelsey L. Pomykala, Jens Kleesiek, Victor Alves, Jan Egger
arXiv
Generation of Synthetic Data: A Generative Adversarial Networks Approach
André Ferreira, Ricardo Magalhães, Victor Alves
Big Data Analytics and Artificial Intelligence in the Healthcare Industry
Generation of Synthetic Rat Brain MRI Scans with a 3D Enhanced Alpha Generative Adversarial Network
André Ferreira, Ricardo Magalhães, Sébastien Mériaux, Victor Alves
Applied Sciences
Radiomics in Head and Neck Cancer Outcome Predictions
Maria Gonçalves, Christina Gsaxner, André Ferreira, Jianning Li, Behrus Puladi, Jens Kleesiek, Jan Egger, Victor Alves
Diagnostics 
