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Zhang, Ray Zirui; Ezhov, Ivan; Balcerak, Michal; Zhu, Andy; Wiestler, Benedikt; Menze, Bjoern; Lowengrub, John S (2025). Personalized predictions of Glioblastoma infiltration: Mathematical models, Physics-Informed Neural Networks and multimodal scans. Medical Image Analysis, 101:103423.
Li, Jianning; Zhou, Zongwei; Yang, Jiancheng; Pepe, Antonio; Gsaxner, Christina; Luijten, Gijs; Qu, Chongyu; Zhang, Tiezheng; Chen, Xiaoxi; Li, Wenxuan; Wodzinski, Marek; Friedrich, Paul; Xie, Kangxian; Jin, Yuan; Ambigapathy, Narmada; Nasca, Enrico; Solak, Naida; Melito, Gian Marco; Vu, Viet Duc; Memon, Afaque R; Schlachta, Christopher; De Ribaupierre, Sandrine; Patel, Rajnikant; Eagleson, Roy; Chen, Xiaojun; Mächler, Heinrich; Kirschke, Jan Stefa; de la Rosa, Ezequiel; Christ, Patrick Ferdinand; Li, Hongwei Bran; et al (2025). $MedShapeNet$ – a large-scale dataset of 3D medical shapes for computer vision. Biomedizinische Technik. Biomedical engineering, 70(1):71-90.
De Nardo, Alessio Nicola. Context Matters: How the Social and Ecological Environment Affects Sexual Selection and Mating System Dynamics in $\textit{Drosophila prolongata }$. 2025, University of Zurich, Faculty of Science.
Ivantsits, Matthias; Goubergrits, Leonid; Kuhnigk, Jan-Martin; Huellebrand, Markus; Bruening, Jan; Kossen, Tabea; Pfahringer, Boris; Schaller, Jens; Spuler, Andreas; Kuehne, Titus; Jia, Yizhuan; Li, Xuesong; Shit, Suprosanna; Menze, Bjoern; Su, Ziyu; Ma, Jun; Nie, Ziwei; Jain, Kartik; Liu, Yanfei; Lin, Yi; Hennemuth, Anja (2025). Corrigendum to “Detection and analysis of cerebral aneurysms based on X-ray rotational angiography - the CADA 2020 challenge” [Medical Image Analysis, April 2022, Volume 77, 102333]. Medical Image Analysis, 100:103363.
Bressan, Dario; IMAXT Cancer Grand Challenges Consortium; Walton, Nicholas; Hannon, Gregory J (2025). Cancer Research in the Age of Spatial Omics: Lessons from IMAXT. Cancer Discovery, 15(1):16-21.
Durrer, Alicia; Wolleb, Julia; Bieder, Florentin; Friedrich, Paul; Melie-Garcia, Lester; Ocampo Pineda, Mario Alberto; Bercea, Cosmin I; Hamamci, Ibrahim Ethem; Wiestler, Benedikt; Piraud, Marie (2025). Denoising diffusion models for 3d healthy brain tissue inpainting. In: Mukhopadhyay, Anirban; Oksuz, Ilkay; Engelhardt, Sandy; Mehrof, Dorit; Yuan, Yixuan. Deep Generative Models: 4th MICCAI Workshop, DGM4MICCAI 2024, Held in Conjunction with MICCAI 2024, Marrakesh, Morocco, October 10, 2024, Proceedings. Heidelberg: Springer (Bücher), 87-97.
Panetti, Camilla. The Co-Inhibitory Receptor TIGIT Confers Tissue Protective Capacity to Tregs. 2024, University of Zurich, Faculty of Science.
Vollenweider, Vera; Rehm, Karoline; Chepkirui, Clara; Pérez-Berlanga, Manuela; Polymenidou, Magdalini; Piel, Jörn; Bigler, Laurent; Kümmerli, Rolf (2024). Antimicrobial activity of iron-depriving pyoverdines against human opportunistic pathogens. eLife, 13:RP92493.
Delgrange, Camille; Demler, Olga; Mora, Samia; Menze, Bjoern; Ezequiel, de la Rosa; Davoudi, Neda (2024). A Self-Supervised Model for Multi-modal Stroke Risk Prediction. In: AIM-FM workshop, Neurips 2024, Vancouver Convention Center, 10 December 2024 - 15 December 2024.
Albarqouni, Shadi; Baumgartner, Christian; Dou, Qi; Konukoglu, Ender; Menze, Bjoern; Venkataraman, Archana (2024). Editorial for the Special Issue on the 2022 Medical Imaging with Deep Learning Conference. Medical Image Analysis, 98:103308.
Bodenmiller, Bernd (2024). Highly multiplexed imaging in the omics era: understanding tissue structures in health and disease. Nature Methods, 21(12):2209-2211.
Girlanda, Francesco; Demler, Olga; Menze, Bjoern; Davoudi, Neda (2024). Enhancing Cardiovascular Disease Prediction through Multi-Modal Self-Supervised Learning. In: British Machine Vision Conference 2024, Glasgow, UK, 25 November 2024 - 28 November 2024.
Hurst, Verena; Gerhold, Christian B; Tarashev, Cleo V D; Challa, Kiran; Seeber, Andrew; Yamazaki, Shota; Knapp, Britta; Helliwell, Stephen B; Bodenmiller, Bernd; Harata, Masahiko; Shimada, Kenji; Gasser, Susan M (2024). Loss of cytoplasmic actin filaments raises nuclear actin levels to drive INO80C-dependent chromosome fragmentation. Nature Communications, 15(1):9910.
Glandorf, Lukas; Wittmann, Bastian; Droux, Jeanne; Glück, Chaim; Weber, Bruno; Wegener, Susanne; El Amki, Mohamad; Leitgeb, Rainer; Menze, Bjoern; Razansky, Daniel (2024). Bessel beam optical coherence microscopy enables multiscale assessment of cerebrovascular network morphology and function. Light: Science & Applications, 13(1):307.
Ivankovic, Ivna. Cell-Free DNA Fragments as Biomarkers in Radiooncology and Gynecology. 2024, University of Zurich, Faculty of Science.
Walter, Natalie Monet. Elucidating the Functional Effects of Omega-3 Fatty Acids with and without Methylphenidate as a Treatment in ADHD. 2024, University of Zurich, Faculty of Science.
Tantardini, Elena. Understanding the Role of FUS in Synaptic RNA Homeostasis in Physiology and Neurodegeneration. 2024, University of Zurich, Faculty of Science.
Bollhagen, Alina; Bodenmiller, Bernd (2024). Highly Multiplexed Tissue Imaging in Precision Oncology and Translational Cancer Research. Cancer Discovery, 14(11):2071-2088.
Marquart, Kim Fabiano; Mathis, Nicolas; Mollaysa, Amina; Müller, Saphira; Kissling, Lucas; Rothgangl, Tanja; Schmidheini, Lukas; Kulcsár, Péter István; Allam, Ahmed; Kaufmann, Masako M; Matsushita, Mai; Haenggi, Tatjana; Cathomen, Toni; Kopf, Manfred; Krauthammer, Michael; Schwank, Gerald (2024). Effective genome editing with an enhanced ISDra2 TnpB system and deep learning-predicted ωRNAs. Nature Methods, 21(11):2084-2093.
Möller, Hendrik; Graf, Robert; Schmitt, Joachim; Keinert, Benjamin; Schön, Hanna; Atad, Matan; Sekuboyina, Anjany; Streckenbach, Felix; Kofler, Florian; Kroencke, Thomas; Bette, Stefanie; Willich, Stefan N; Keil, Thomas; Niendorf, Thoralf; Pischon, Tobias; Endemann, Beate; Menze, Bjoern; Rueckert, Daniel; Kirschke, Jan S (2024). SPINEPS—automatic whole spine segmentation of T2-weighted MR images using a two-phase approach to multi-class semantic and instance segmentation. European Radiology, 35(3):1178-1189.
Prabhakar, Chinmay; Shit, Suprosanna; Musio, Fabio; Yang, Kaiyuan; Amiranashvili, Tamaz; Paetzold, Johannes C; Li, Hongwei Bran; Menze, Bjoern (2024). 3D Vessel Graph Generation Using Denoising Diffusion. In: Linguraru, Marius George; Dou, Qi; Feragen, Aasa; Giannarou, Stamatia; Glocker, Ben; Lekadir, Karim; Schnabel, Julia A. Medical Image Computing and Computer Assisted Intervention – MICCAI 2024 (1. Auflage). Cham: Springer (Bücher), 3-13.
Hamamci, Ibrahim Ethem; Er, Sezgin; Menze, Bjoern (2024). CT2Rep: Automated radiology report generation for 3d medical imaging. In: Linguraru, Marius George; Dou, Qi; Feragen, Aasa; Giannarou, Stamatia; Glocker, Ben; Lekadir, Karim; Schnabel, Julia A. Medical Image Computing and Computer Assisted Intervention – MICCAI 2024. Cham: Springer (Bücher), 476-486.
Wittmann, Bastian; Glandorf, Lukas; Paetzold, Johannes C; Amiranashvili, Tamaz; Wälchli, Thomas; Razansky, Daniel; Menze, Bjoern (2024). Simulation-Based Segmentation of Blood Vessels in Cerebral 3D OCTA Images. In: Linguraru, Marius George; Dou, Qi; Feragen, Aasa; Giannarou, Stamatia; Glocker, Ben; Lekadir, Karim; Schnabel, Julia A. Medical Image Computing and Computer Assisted Intervention – MICCAI 2024. Cham: Springer (Bücher), 645-655.
Esposito, Mauro; Yerly, Laura; Shukla, Prachi; Hermes, Victoria; Sella, Federica; Balazs, Zsolt; Lattmann, Evelyn; Tastanova, Aizhan; Turko, Patrick; Lang, Ramon; Kolm, Isabel; Staeger, Ramon; Kuonen, François; Krauthammer, Michael; Hafner, Juerg; Levesque, Mitchell P; Restivo, Gaetana (2024). COL10A1 expression distinguishes a subset of cancer-associated fibroblasts present in the stroma of high-risk basal cell carcinoma. British Journal of Dermatology, 191(5):775-790.
Vollenweider, Vera; Roncoroni, Flavie; Kümmerli, Rolf (2024). Pyoverdine–antibiotic combination treatment: its efficacy and effects on resistance evolution in $Escherichia$ $coli$. microLife, 5:uqae021.
Huang, Yuqing; Wittmann, Bastian; Demler, Olga; Menze, Bjoern; Davoudi, Neda (2024). Predicting stroke through retinal graphs and multimodal self-supervised learning. In: MICCAI 2024 - ML-CDS 2024: Multimodal Learning and Fusion Across Scales for Clinical Decision Support, Marrakesh, Morocco, 6 October 2024 - 10 October 2024.
Gu, Shaohua; Shao, Yuanzhe; Rehm, Karoline; Bigler, Laurent; Zhang, Di; He, Ruolin; Xu, Ruichen; Shao, Jiqi; Jousset, Alexandre; Friman, Ville-Petri; Bian, Xiaoying; Wei, Zhong; Kümmerli, Rolf; Li, Zhiyuan (2024). Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways. eLife, 13:RP96719.
Laffont, Clémentine; Wechsler, Tobias; Kümmerli, Rolf (2024). Interactions between $Pseudomonas$ $aeruginosa$ and six opportunistic pathogens cover a broad spectrum from mutualism to antagonism. Environmental Microbiology Reports, 16(5):e70015.
Prélot, Laurie. In-Silico Prediction of Splicing-Derived Neoepitope Candidates. 2024, ETH Zurich.
Cords, Lena; de Souza, Natalie; Bodenmiller, Bernd (2024). Classifying cancer-associated fibroblasts-The good, the bad, and the target. Cancer Cell, 42(9):1480-1485.
Arekatla, Geethika; Skylaki, Stavroula; Corredor Suarez, David; Jackson, Hartland; Schapiro, Denis; Engler, Stefanie; Auler, Markus; Camargo Ortega, German; Hastreiter, Simon; Reimann, Andreas; Loeffler, Dirk; Bodenmiller, Bernd; Schroeder, Timm (2024). Identification of an embryonic differentiation stage marked by Sox1 and FoxA2 co-expression using combined cell tracking and high dimensional protein imaging. Nature Communications, 15(1):7860.
Buchner, Josef A; Kofler, Florian; Mayinger, Michael; Christ, Sebastian M; Brunner, Thomas B; Wittig, Andrea; Menze, Bjoern; Zimmer, Claus; Meyer, Bernhard; Guckenberger, Matthias; Andratschke, Nicolaus; El Shafie, Rami A; Debus, Jürgen; Rogers, Susanne; Riesterer, Oliver; Schulze, Katrin; Feldmann, Horst J; Blanck, Oliver; Zamboglou, Constantinos; Ferentinos, Konstantinos; Bilger-Zähringer, Angelika; Grosu, Anca L; Wolff, Robert; Piraud, Marie; Eitz, Kerstin A; Combs, Stephanie E; Bernhardt, Denise; Rueckert, Daniel; Wiestler, Benedikt; Peeken, Jan C (2024). Radiomics-based prediction of local control in patients with brain metastases following postoperative stereotactic radiotherapy. Neuro-Oncology, 26(9):1638-1650.
Frei, Anja Laura. Tumor and Immune Profiling by Image Analysis and Digital Pathology. 2024, University of Zurich, Faculty of Science.
Mathis, Nicolas; Allam, Ahmed; Tálas, András; Kissling, Lucas; Benvenuto, Elena; Schmidheini, Lukas; Schep, Ruben; Damodharan, Tanav; Balázs, Zsolt; Janjuha, Sharan; Ioannidi, Eleonora I; Böck, Desirée; van Steensel, Bas; Krauthammer, Michael; Schwank, Gerald (2024). Publisher Correction: Machine learning prediction of prime editing efficiency across diverse chromatin contexts. Nature Biotechnology:Epub ahead of print.
Schmitz, Désirée A; Wechsler, Tobias; Li, Hongwei Bran; Menze, Bjoern H; Kümmerli, Rolf (2024). A new protocol for multispecies bacterial infections in zebrafish and their monitoring through automated image analysis. PLoS ONE, 19(8):e0304827.
Peeken, Jan C; Etzel, Lucas; Tomov, Tim; Münch, Stefan; Schüttrumpf, Lars; Shaktour, Julius H; Kiechle, Johannes; Knebel, Carolin; Schaub, Stephanie K; Mayr, Nina A; Woodruff, Henry C; Lambin, Philippe; Gersing, Alexandra S; Bernhardt, Denise; Nyflot, Matthew J; Menze, Bjoern; Combs, Stephanie E; Navarro, Fernando (2024). Development and benchmarking of a Deep Learning-based MRI-guided gross tumor segmentation algorithm for Radiomics analyses in extremity soft tissue sarcomas. Radiotherapy and Oncology, 197:110338.
Balázs, Zsolt; Balermpas, Panagiotis; Ivanković, Ivna; Willmann, Jonas; Gitchev, Todor; Bryant, Asher; Guckenberger, Matthias; Krauthammer, Michael; Andratschke, Nicolaus (2024). Longitudinal cell-free DNA characterization by low-coverage whole-genome sequencing in patients undergoing high-dose radiotherapy. Radiotherapy and Oncology, 197:110364.
Kaltenecker, Doris; Al-Maskari, Rami; Negwer, Moritz; Hoeher, Luciano; Kofler, Florian; Zhao, Shan; Todorov, Mihail; Rong, Zhouyi; Paetzold, Johannes Christian; Wiestler, Benedikt; Piraud, Marie; Rueckert, Daniel; Geppert, Julia; Morigny, Pauline; Rohm, Maria; Menze, Bjoern H; Herzig, Stephan; Berriel Diaz, Mauricio; Ertürk, Ali (2024). Virtual reality-empowered deep-learning analysis of brain cells. Nature Methods, 21(7):1306-1315.
Mathis, Nicolas; Allam, Ahmed; Tálas, András; Kissling, Lucas; Benvenuto, Elena; Schmidheini, Lukas; Schep, Ruben; Damodharan, Tanav; Balazs, Zsolt; Janjuha, Sharan; Ioannidi, Eleonora I; Böck, Desirée; van Steensel, Bas; Krauthammer, Michael; Schwank, Gerald (2024). Machine learning prediction of prime editing efficiency across diverse chromatin contexts. Nature Biotechnology:Epub ahead of print.
Zbinden, Aurélie. Implications of TDP-43 RNA Binding in Physiology and Pathology. 2024, University of Zurich, Faculty of Science.
Rakebrandt, Nikolas; Yassini, Nima; Kolz, Anna; Schorer, Michelle; Lambert, Katharina; Goljat, Eva; Estrada Brull, Anna; Rauld, Celine; Balazs, Zsolt; Krauthammer, Michael; Carballido, José M; Peters, Anneli; Joller, Nicole (2024). Innate acting memory Th1 cells modulate heterologous diseases. Proceedings of the National Academy of Sciences of the United States of America, 121(24):e2312837121.
He, Hailong; Paetzold, Johannes C; Börner, Nils; Riedel, Erik; Gerl, Stefan; Schneider, Simon; Fisher, Chiara; Ezhov, Ivan; Shit, Suprosanna; Li, Hongwei; Rückert, Daniel; Aguirre, Juan; Biedermann, Tilo; Darsow, Ulf; Menze, Bjoern; Ntziachristos, Vasilis (2024). Machine Learning Analysis of Human Skin by Optoacoustic Mesoscopy for Automated Extraction of Psoriasis and Aging Biomarkers. IEEE Transactions on Medical Imaging, 43(6):2074-2085.
Kreitner, Linus; Paetzold, Johannes C; Rauch, Nikolaus; Chen, Chen; Hagag, Ahmed M; Fayed, Alaa E; Sivaprasad, Sobha; Rausch, Sebastian; Weichsel, Julian; Menze, Bjoern H; Harders, Matthias; Knier, Benjamin; Rueckert, Daniel; Menten, Martin J (2024). Synthetic Optical Coherence Tomography Angiographs for Detailed Retinal Vessel Segmentation Without Human Annotations. IEEE Transactions on Medical Imaging, 43(6):2061-2073.
Trottet, Cécile; Allam, Ahmed; Horvath, Aron N; Finckh, Axel; Hügle, Thomas; Adler, Sabine; Kyburz, Diego; Micheroli, Raphael; Krauthammer, Michael; Ospelt, Caroline (2024). Explainable deep learning for disease activity prediction in chronic inflammatory joint diseases. PLOS Digital Health, 3(6):e0000422.
LaBella, Dominic; Khanna, Omaditya; McBurney-Lin, Shan; Mclean, Ryan; Nedelec, Pierre; Rashid, Arif S; Tahon, Nourel hoda; Altes, Talissa; Baid, Ujjwal; Bhalerao, Radhika; Dhemesh, Yaseen; Floyd, Scott; Godfrey, Devon; Hilal, Fathi; Janas, Anastasia; Kazerooni, Anahita; Kent, Collin; Kirkpatrick, John; Kofler, Florian; Leu, Kevin; Maleki, Nazanin; Menze, Bjoern; Pajot, Maxence; Reitman, Zachary J; Rudie, Jeffrey D; Saluja, Rachit; Velichko, Yury; Wang, Chunhao; Warman, Pranav I; Sollmann, Nico; et al (2024). A multi-institutional meningioma MRI dataset for automated multi-sequence image segmentation. Scientific Data, 11(1):496.
Vollenweider, Vera. Pyoverdines: Novel Antimicrobial Compounds against Human Bacterial Pathogens. 2024, University of Zurich, Faculty of Science.
Amiranashvili, Tamaz; Lüdke, David; Li, Hongwei Bran; Zachow, Stefan; Menze, Bjoern H (2024). Learning continuous shape priors from sparse data with neural implicit functions. Medical Image Analysis, 94:103099.
Fidon, Lucas; Aertsen, Michael; Kofler, Florian; Bink, Andrea; David, Anna L; Deprest, Thomas; Emam, Doaa; Guffens, Frédéric; Jakab, András; Kasprian, Gregor; Kienast, Patric; Melbourne, Andrew; Menze, Bjoern; Mufti, Nada; Pogledic, Ivana; Prayer, Daniela; Stuempflen, Marlene; Van Elslander, Esther; Ourselin, Sébastien; Deprest, Jan; Vercauteren, Tom (2024). A Dempster-Shafer Approach to Trustworthy AI With Application to Fetal Brain MRI Segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence, 46(5):3784-3795.
Mridha, Subham; Wechsler, Tobias; Kümmerli, Rolf (2024). Space and genealogy determine inter-individual differences in siderophore gene expression in bacterial colonies. Cell Reports, 43(4):114106.
Watson, Spencer S; Duc, Benoit; Kang, Ziqi; de Tonnac, Axel; Eling, Nils; Font, Laure; Whitmarsh, Tristan; Massara, Matteo; IMAXT Consortium; Bodenmiller, Bernd; Hausser, Jean; Joyce, Johanna A (2024). Microenvironmental reorganization in brain tumors following radiotherapy and recurrence revealed by hyperplexed immunofluorescence imaging. Nature Communications, 15(1):3226.
Vladimirov, Nikita; Voigt, Fabian F; Naert, Thomas; Araujo, Gabriela R; Cai, Ruiyao; Reuss, Anna Maria; Zhao, Shan; Schmid, Patricia; Hildebrand, Sven; Schaettin, Martina; Groos, Dominik; Mateos, José María; Bethge, Philipp; Yamamoto, Taiyo; Aerne, Valentino; Roebroeck, Alard; Ertürk, Ali; Aguzzi, Adriano; Ziegler, Urs; Stoeckli, Esther; Baudis, Laura; Lienkamp, Soeren S; Helmchen, Fritjof (2024). Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for cleared samples. Nature Communications, 15(1):2679.
Ruchti, Fiorella. Immunity to the Skin Commensal Yeast $\textit{Malassezia}$ in Healthy and Atopic Skin. 2024, University of Zurich, Faculty of Science.
Komninou, Maria Angeliki; Egli, Simon; Rossi, Aurelio; Ernst, Jutta; Krauthammer, Michael; Schuepbach, Reto A; Delgado, Marcos; Bartussek, Jan (2024). Former smoking, but not active smoking, is associated with delirium in postoperative ICU patients: a matched case-control study. Frontiers in Psychiatry, 15:1347071.
Cords, Lena; Engler, Stefanie; Haberecker, Martina; Rüschoff, Jan Hendrik; Moch, Holger; de Souza, Natalie; Bodenmiller, Bernd (2024). Cancer-associated fibroblast phenotypes are associated with patient outcome in non-small cell lung cancer. Cancer Cell, 42(3):396-412.e5.
de Souza, Natalie; Zhao, Shan; Bodenmiller, Bernd (2024). Multiplex protein imaging in tumour biology. Nature Reviews Cancer, 24(3):171-191.
Kirchberger, Stefanie; Shoeb, Mohamed R; Lazic, Daria; Wenninger-Weinzierl, Andrea; Fischer, Kristin; Shaw, Lisa E; Nogueira, Filomena; Rifatbegovic, Fikret; Bozsaky, Eva; Ladenstein, Ruth; Bodenmiller, Bernd; Lion, Thomas; Traver, David; Farlik, Matthias; Schöfer, Christian; Taschner-Mandl, Sabine; Halbritter, Florian; Distel, Martin (2024). Comparative transcriptomics coupled to developmental grading via transgenic zebrafish reporter strains identifies conserved features in neutrophil maturation. Nature Communications, 15(1):1792.
Joller, Nicole; Anderson, Ana C; Kuchroo, Vijay K (2024). LAG-3, TIM-3, and TIGIT: Distinct functions in immune regulation. Immunity, 57(2):206-222.
Fontana, Elena; Bongianni, Matilde; Benussi, Alberto; Bronzato, Erika; Scialo, Carlo; Sacchetto, Luca; Cagnin, Annachiara; Castriciano, Santina; Buratti, Emanuele; Gardoni, Fabrizio; Italia, Maria; Schreiber, Alberto; Ferracin, Chiara; Fiorini, Michele; Newell, Kathy L; Cracco, Laura; Garringer, Holly J; Cecchini, Maria Paola; Polymenidou, Magdalini; Padovani, Alessandro; Monaco, Salvatore; Legname, Giuseppe; Ghetti, Bernardino; Borroni, Barbara; Zanusso, Gianluigi (2024). Detection of TDP-43 seeding activity in the olfactory mucosa from patients with frontotemporal dementia. Alzheimer's & Dementia, 20(2):1156-1165.
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; Antonelli, Michela; Arbel, Tal; Bakas, Spyridon; Benis, Arriel; Blaschko, Matthew B; Cardoso, M Jorge; Cheplygina, Veronika; Cimini, Beth A; Collins, Gary S; Farahani, Keyvan; et al (2024). Metrics reloaded: recommendations for image analysis validation. Nature Methods, 21(2):195-212.
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; Ferrer, Luciana; Galdran, Adrian; van Ginneken, Bram; Glocker, Ben; Godau, Patrick; Hashimoto, Daniel A; Hoffman, Michael M; Huisman, Merel; Isensee, Fabian; Jannin, Pierre; et al (2024). Understanding metric-related pitfalls in image analysis validation. Nature Methods, 21(2):182-194.
Frommenwiler, Joel. Variation in antibiotic susceptibility and virulence factor expression among bacterial pathogens isolated from burn wounds. 2024, University of Zurich, Faculty of Science.
Wang, Nanqi; Wang, Tianqi; Chen, Yu; Wang, Ming; Lu, Qiaofang; Wang, Kunguang; Dou, Zhechao; Chi, Zhiguang; Qiu, Wei; Dai, Jing; Niu, Lei; Cui, Jianyu; Wei, Zhong; Zhang, Fusuo; Kümmerli, Rolf; Zuo, Yuanmei (2024). Microbiome convergence enables siderophore-secreting-rhizobacteria to improve iron nutrition and yield of peanut intercropped with maize. Nature Communications, 15(1):839.
Schmitz, Désirée A; Wechsler, Tobias; Mignot, Ingrid; Kümmerli, Rolf (2024). Predicting bacterial interaction outcomes from monoculture growth and supernatant assays. ISME Communications, 4(1):ycae045.
Meyer, Lasse; Eling, Nils; Bodenmiller, Bernd (2024). cytoviewer: an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data. BMC Bioinformatics, 25(1):9.
Balázs, Zsolt; Gitchev, Todor; Ivanković, Ivna; Krauthammer, Michael (2024). Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis. Bioinformatics, 40(1):btae017.
Weidner, Jonas; Ezhov, Ivan; Balcerak, Michal; Metz, Marie-Christin; Litvinov, Sergey; Kaltenbach, Sebastian; Feiner, Leonhard; Lux, Laurin; Kofler, Florian; Lipkova, Jana; Latz, Jonas; Rueckert, Daniel; Menze, Bjoern; Wiestler, Benedikt (2024). A Learnable Prior Improves Inverse Tumor Growth Modeling. IEEE Transactions on Medical Imaging:Epub ahead of print.
Wiltgen, Tun; McGinnis, Julian; Schlaeger, Sarah; Kofler, Florian; Voon, CuiCi; Berthele, Achim; Bischl, Daria; Grundl, Lioba; Will, Nikolaus; Metz, Marie; Schinz, David; Sepp, Dominik; Prucker, Philipp; Schmitz-Koep, Benita; Zimmer, Claus; Menze, Bjoern; Rueckert, Daniel; Hemmer, Bernhard; Kirschke, Jan; Mühlau, Mark; Wiestler, Benedikt (2024). LST-AI: A deep learning ensemble for accurate MS lesion segmentation. NeuroImage: Clinical, 42:103611.
Susmelj, Anna Klimovskaia; Lafci, Berkan; Ozdemir, Firat; Davoudi, Neda; Deán-Ben, Xosé Luís; Perez-Cruz, Fernando; Razansky, Daniel (2024). Signal domain adaptation network for limited-view optoacoustic tomography. Medical Image Analysis, 91:103012.
Sudre, Carole H; Van Wijnen, Kimberlin; Dubost, Florian; Adams, Hieab; Atkinson, David; Barkhof, Frederik; Birhanu, Mahlet A; Bron, Esther E; Camarasa, Robin; Chaturvedi, Nish; Chen, Yuan; Chen, Zihao; Chen, Shuai; Dou, Qi; Evans, Tavia; Ezhov, Ivan; Gao, Haojun; Girones Sanguesa, Marta; Gispert, Juan Domingo; Gomez Anson, Beatriz; Hughes, Alun D; Ikram, M Arfan; Ingala, Silvia; Jaeger, H Rolf; Kofler, Florian; Kuijf, Hugo J; Kutnar, Denis; Lee, Minho; Li, Bo; Lorenzini, Luigi; et al (2024). Where is VALDO? VAscular Lesions Detection and segmentatiOn challenge at MICCAI 2021. Medical Image Analysis, 91:103029.
Gaudin, Robert; Vinayahalingam, Shankeeth; van Nistelrooij, Niels; Ghanad, Iman; Otto, Wolfus; Kewenig, Stephan; Rendenbach, Carsten; Alevizakos, Vasilios; Grün, Pascal; Kofler, Florian (2024). AI-Powered Identification of Osteoporosis in Dental Panoramic Radiographs: Addressing Methodological Flaws in Current Research. Diagnostics, 14(20):2298.
Winterhalter, Laura; Kofler, Florian; Ströbele, Dragan-Alexander; Othman, Ahmed; von See, Constantin (2024). AI-assisted diagnostics in dentistry: An eye-tracking study on user behavior. Journal of Clinical and Experimental Dentistry, 16(5):e547.
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Antonelli, Michela; Reinke, Annika; Bakas, Spyridon; Farahani, Keyvan; Kopp-Schneider, Annette; Landman, Bennett A; Litjens, Geert; Menze, Bjoern; Ronneberger, Olaf; Summers, Ronald M; van Ginneken, Bram; Bilello, Michel; Bilic, Patrick; Christ, Patrick F; Do, Richard K G; Gollub, Marc J; Heckers, Stephan H; Huisman, Henkjan; Jarnagin, William R; McHugo, Maureen K; Napel, Sandy; Pernicka, Jennifer S Golia; Rhode, Kawal; Tobon-Gomez, Catalina; Vorontsov, Eugene; Meakin, James A; Ourselin, Sébastien; Wiesenfarth, Manuel; Arbeláez, Pablo; Bae, Byeonguk; et al (2022). The Medical Segmentation Decathlon. Nature Communications, 13(1):4128.
Kofler, Florian; et al; Menze, Bjoern (2022). blob loss: instance imbalance aware loss functions for semantic segmentation. ArXiv.org 2205.08209, Cornell University.
Navarro, Fernando; Sasahara, Guido; Shit, Suprosanna; Sekuboyina, Anjany; Ezhov, Ivan; Peeken, Jan C; Combs, Stephanie E; Menze, Bjoern H (2022). A Unified 3D Framework for Organs-at-Risk Localization and Segmentation for Radiation Therapy Planning. In: 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Glasgow, Scotland, United Kingdom, 11 July 2022 - 15 July 2022. Institute of Electrical and Electronics Engineers, 1544-1547.
Navarro, Fernando; Watanabe, Christopher; Shit, Suprosanna; Sekuboyina, Anjany; Peeken, Jan C; Combs, Stephanie E; Menze, Bjoern H (2022). Self-Supervised Pretext Tasks in Model Robustness & Generalizability: A Revisit from Medical Imaging Perspective. In: 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Glasgow, Scotland, United Kingdom, 11 July 2022 - 15 July 2022. Institute of Electrical and Electronics Engineers, 5074-5079.
Fidon, Lucas; et al; Menze, Bjoern (2022). A Dempster-Shafer approach to trustworthy AI with application to fetal brain MRI segmentation. ArXiv.org 2204.02779, Cornell University.
Maier-Hein, Lena; et al; Menze, Bjoern (2022). Metrics reloaded: Pitfalls and recommendations for image analysis validation. ArXiv.org 2206.01653, Cornell University.
Amiranashvili, Tamaz; Lüdke, D; Liu, H B; Menze, Bjoern; Zachow, S (2022). Learning Shape Reconstruction from Sparse Measurements with Neural Implicit Functions. In: MIDL 2022, Zurich Switzerland, 6 July 2022. MLResearch Press, 1-13.
Kenigsbuch, Mor; Bost, Pierre; Halevi, Shahar; Chang, Yuzhou; Chen, Shuo; Ma, Qin; Hajbi, Renana; Schwikowski, Benno; Bodenmiller, Bernd; Fu, Hongjun; Schwartz, Michal; Amit, Ido (2022). A shared disease-associated oligodendrocyte signature among multiple CNS pathologies. Nature Neuroscience, 25(7):876-886.
Sollmann, Nico; Löffler, Maximilian T; El Husseini, Malek; Sekuboyina, Anjany; Dieckmeyer, Michael; Rühling, Sebastian; Zimmer, Claus; Menze, Bjoern; Joseph, Gabby B; Baum, Thomas; Kirschke, Jan S (2022). Automated Opportunistic Osteoporosis Screening in Routine Computed Tomography of the Spine: Comparison With Dedicated Quantitative CT. Journal of Bone and Mineral Research, 37(7):1287-1296.
Soichot, Julien; Guttmann, Nathalie; Rehrauer, Hubert; Joller, Nicole; Tritten, Lucienne (2022). Nematode microRNAs can Individually Regulate Interferon Regulatory Factor 4 and mTOR in Differentiating T Helper 2 Lymphocytes and Modulate Cytokine Production in Macrophages. Frontiers in Molecular Biosciences, 9:909312.
Ivankovic, Ivana; Balázs, Zsolt; Gitchev, Todor; Trejo Banos, Daniel; Moldovan, Norbert; Panagiotis, Balermpas; Willmann, Jonas; Andratschke, N; Moulière, Florent; Krauthammer, Michael (2022). A versatile computational pipeline for the preprocessing of cell-free DNA fragmentation data. Cancer Research 82, University of Zurich.
de la Rosa, Ezequiel; et al; Menze, Bjoern H (2022). Detecting CTP Truncation Artifacts in Acute Stroke Imaging from the Arterial Input and the Vascular Output Functions. medRxiv 22276371, Cold Spring Harbor Laboratory.
Ivankovic, Ivna; Balázs, Zsolt; Gitchev, Todor; Banos, Daniel Trejo; Moldovan, Norbert; Balermpas, Panagiotis; Willmann, Jonas; Andratschke, Nicolaus; Moulière, Florent; Krauthammer, Michael (2022). Abstract 1912: A versatile computational pipeline for the preprocessing of cell-free DNA fragmentation data. Cancer Research, 82(12_Supplem):1912.
Petzsche, Moritz Roman Hernandez; et al; Kofler, Florian; Ezhov, Ivan; Menze, Bjoern (2022). ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset. ArXiv.org 2206.06694, Cornell University.
Al Boustani, George; Weiß, Lennart Jakob Konstantin; Li, Hongwei; Meyer, Svea Marie; Hiendlmeier, Lukas; Rinklin, Philipp; Menze, Bjoern; Hemmert, Werner; Wolfrum, Bernhard (2022). Influence of Auditory Cues on the Neuronal Response to Naturalistic Visual Stimuli in a Virtual Reality Setting. Frontiers in Human Neuroscience, 16:809293.
Dieckmeyer, Michael; Löffler, Maximilian Thomas; El Husseini, Malek; Sekuboyina, Anjany; Menze, Bjoern; Sollmann, Nico; Wostrack, Maria; Zimmer, Claus; Baum, Thomas; Kirschke, Jan Stefan (2022). Level-Specific Volumetric BMD Threshold Values for the Prediction of Incident Vertebral Fractures Using Opportunistic QCT: A Case-Control Study. Frontiers in Endocrinology, 13:882163.
Kofler, Florian; et al; Menze, Bjoern (2022). Deep Quality Estimation: Creating Surrogate Models for Human Quality Ratings. ArXiv.org 2205.10355, Cornell University.
Wiersma, Vera I; Rigort, Ruben; Polymenidou, Magdalini (2022). Tau: a phase in the crowd. The EMBO Journal, 41:e111425.
Mridha, Subham; Kümmerli, Rolf (2022). Enforced specialization fosters mutual cheating and not division of labour in the bacterium Pseudomonas aeruginosa. Journal of Evolutionary Biology, 35(5):719-730.
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Danenberg, Esther; Bardwell, Helen; Zanotelli, Vito R T; Provenzano, Elena; Chin, Suet-Feung; Rueda, Oscar M; Green, Andrew; Rakha, Emad; Aparicio, Samuel; Ellis, Ian O; Bodenmiller, Bernd; Caldas, Carlos; Ali, H Raza (2022). Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature Genetics, 54(5):660-669.
Pastor Arroyo, Eva Maria; Yassini, Nima; Sakiri, Elif; Russo, Giancarlo; Bourgeois, Soline; Mohebbi, Nilufar; Amann, Kerstin; Joller, Nicole; Wagner, Carsten A; Imenez Silva, Pedro Henrique (2022). Alkali therapy protects renal function, suppresses inflammation, and improves cellular metabolism in kidney disease. Clinical Science, 136(8):557-577.
Estrada Brull, Anna; Panetti, Camilla; Joller, Nicole (2022). Moving to the Outskirts: Interplay Between Regulatory T Cells and Peripheral Tissues. Frontiers in Immunology, 13:864628.
Xue, Song; Gafita, Andrei; Dong, Chao; Zhao, Yu; Tetteh, Giles; Menze, Bjoern H; Ziegler, Sibylle; Weber, Wolfgang; Afshar-Oromieh, Ali; Rominger, Axel; Eiber, Matthias; Shi, Kuangyu (2022). Proof-of-concept Study to Estimate Individual Post-Therapy Dosimetry in Men with Advanced Prostate Cancer Treated with 177Lu-PSMA I&T Therapy. Research Square 1588151/v1, University of Zurich.
Yuan, Han; Liu, Minxuan; Kang, Lican; Chenkui, Miao; Wu, Ying; et al; Krauthammer, Michael (2022). An empirical study of the effect of background data size on the stability of SHapley Additive exPlanations (SHAP) for deep learning models. ArXiv.org 2204.11351, Cornell University.
Jayakumar, Priyanikha; Figueiredo, Alexandre R T; Kümmerli, Rolf (2022). Evolution of the quorum sensing systems in Pseudomonas aeruginosa can involve both loss of regulon function and network modulation. bioRxiv 489656, Cold Spring Harbor Laboratory.
Finck, Tom; Li, Hongwei; Schlaeger, Sarah; Grundl, Lioba; Sollmann, Nico; Bender, Benjamin; Bürkle, Eva; Zimmer, Claus; Kirschke, Jan; Menze, Björn; Mühlau, Mark; Wiestler, Benedikt (2022). Uncertainty-Aware and Lesion-Specific Image Synthesis in Multiple Sclerosis Magnetic Resonance Imaging: A Multicentric Validation Study. Frontiers in Neuroscience, 16:889808.
de Vargas Roditi, Laura; Jacobs, Andrea; Rueschoff, Jan H; Bankhead, Pete; Chevrier, Stéphane; Jackson, Hartland Warren; Hermanns, Thomas; Fankhauser, Christian Daniel; Poyet, Cédric; Chun, Felix; Rupp, Niels J; Tschaebunin, Alexandra; Bodenmiller, Bernd; Wild, Peter Johannes (2022). Single-cell proteomics defines the cellular heterogeneity of localized prostate cancer. Cell Reports Medicine, 3(4):100604.
Bieri, Uwe; Scharl, Michael; Sigg, Silvan; Szczerba, Barbara Maria; Morsy, Yasser; Rüschoff, Jan Hendrik; Schraml, Peter Hans; Krauthammer, Michael; Hefermehl, Lukas John; Eberli, Daniel; Poyet, Cédric (2022). Prospective observational study of the role of the microbiome in BCG responsiveness prediction (SILENT-EMPIRE): a study protocol. BMJ Open, 12(4):e061421.
Hiltbrunner, Stefanie; Cords, Lena; Kasser, Sabrina; Freiberger, Sandra N; Kreutzer, Susanne; Toussaint, Nora C; Grob, Linda; Opitz, Isabelle; Messerli, Michael; Zoche, Martin; Soltermann, Alex; Rechsteiner, Markus; van den Broek, Maries; Bodenmiller, Bernd; Curioni-Fontecedro, Alessandra (2022). Acquired resistance to anti-PD1 therapy in patients with NSCLC reveals changes in T cell phenotypes and MET amplification. bioRxiv 487590v1, Cold Spring Harbor Laboratory.
Rühling, Sebastian; Scharr, Andreas; Sollmann, Nico; Wostrack, Maria; Löffler, Maximilian T; Menze, Bjoern; Sekuboyina, Anjany; El Husseini, Malek; Braren, Rickmer; Zimmer, Claus; Kirschke, Jan S (2022). Proposed diagnostic volumetric bone mineral density thresholds for osteoporosis and osteopenia at the cervicothoracic spine in correlation to the lumbar spine. European Radiology, 32(9):6207-6214.
Ivantsits, Matthias; Goubergrits, Leonid; Menze, Bjoern; et al (2022). Detection and analysis of cerebral aneurysms based on X-ray rotational angiography - the CADA 2020 challenge. Medical Image Analysis, 77:102333.
Pirkl, Carolin M; Cencini, Matteo; Kurzawski, Jan W; Waldmannstetter, Diana; Li, Hongwei; Sekuboyina, Anjany; Endt, Sebastian; Peretti, Luca; Donatelli, Graziella; Pasquariello, Rosa; Costagli, Mauro; Buonincontri, Guido; Tosetti, Michela; Menzel, Marion I; Menze, Bjoern H (2022). Learning residual motion correction for fast and robust 3D multiparametric MRI. Medical Image Analysis, 77:102387.
Hoch, Tobias; Schulz, Daniel; Eling, Nils; Gómez, Julia Martínez; Levesque, Mitchell P; Bodenmiller, Bernd (2022). Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology, 7(70):eabk1692.
Kaushik, Sandeep S; Bylun, Mikael; Cozzin, Cristina; Shanbhag, Dattesh; Petit, Steven F; Wyatt, Jonathan J; Menzel, Marion I; Pirkl, Carolin M; Mehta, Bhairav; Chauhan, Vikas; Chandrasekharan, Kesavadas; Jonsson, Jojakim; Nyholm, Tufve; Wiesinger, Florian; Menze, Bjoern H (2022). Region of Interest focused MRI to Synthetic CT Translation using Regression and Classification Multi-task Network. ArXiv.org 2203.16288, Cornell University.
Shit, Suprosanna; Koner, Rajat; Wittmann, Bastian; Paetzold, Johannes C; Ezhov, Ivan; Li, Hongwei; Pan, Jiazhen; Sharifzadeh, Sahand; Kaissis, Georgios; Tresp, Volker; Menze, Bjoern (2022). Relationformer: A Unified Framework for Image-to-Graph Generation. ArXiv.org 10202, Cornell University.
Avar, Merve; Heinzer, Daniel; Thackray, Alana M; Liu, Yingjun; Hruska-Plochan, Marian; Sellitto, Stefano; Schaper, Elke; Pease, Daniel Patrick; Yin, Jiang-An; Lakkaraju, Asvin K K; Emmenegger, Marc; Losa, Marco; Chincisan, Andra; Hornemann, Simone Alexandra; Polymenidou, Magdalini; Bujdoso, Raymond; Aguzzi, Adriano (2022). An Arrayed Genome-Wide Perturbation Screen Identifies the Ribonucleoprotein hnRNP K As Rate-Limiting for Prion Propagation. bioRxiv 482765, Cold Spring Harbor Laboratory.
Rehm, Karoline; Vollenweider, Vera; Kümmerli, Rolf; Bigler, Laurent (2022). A comprehensive method to elucidate pyoverdines produced by fluorescent Pseudomonas spp. by UHPLC-HR-MS/MS. Analytical and Bioanalytical Chemistry, 414(8):2671-2685.
Navarro, Fernando; Sasahara, Guido; Shit, Suprosanna; Ezhov, Ivan; Peeken, Jan C; Combs, Stephanie E; Menze, Bjoern H (2022). A unified 3D framework for Organs at Risk Localization and Segmentation for Radiation Therapy Planning. ArXiv.org 00624, Cornell University.
Biller-Andorno, Nikola; Ferrario, Andrea; Joebges, Susanne; Krones, Tanja; Massini, Federico; Barth, Phyllis; Arampatzis, Georgios; Krauthammer, Michael (2022). AI support for ethical decision-making around resuscitation: proceed with care. Journal of Medical Ethics, 48(3):175-183.
Rühling, Sebastian; Navarro, Fernando; Sekuboyina, Anjany; El Husseini, Malek; Baum, Thomas; Menze, Bjoern; Braren, Rickmer; Zimmer, Claus; Kirschke, Jan S (2022). Automated detection of the contrast phase in MDCT by an artificial neural network improves the accuracy of opportunistic bone mineral density measurements. European Radiology, 32(3):1465-1474.
Thomas, Marie Franziska; Kofler, Florian; Grundl, Lioba; Finck, Tom; Li, Hongwei; Zimmer, Claus; Menze, Björn; Wiestler, Benedikt (2022). Improving Automated Glioma Segmentation in Routine Clinical Use Through Artificial Intelligence-Based Replacement of Missing Sequences With Synthetic Magnetic Resonance Imaging Scans. Investigative Radiology, 57(3):187-193.
Lipková, Jana; Menze, Bjoern; Wiestler, Benedikt; Koumoutsakos, Petros; Lowengrub, John S (2022). Modelling glioma progression, mass effect and intracranial pressure in patient anatomy. Journal of the Royal Society Interface, 19(188):20210922.
Bost, Pierre; Schulz, Daniel; Engler, Stefanie; Wasserfall, Clive H; Bodenmiller, Bernd (2022). Optimizing multiplexed imaging experimental design through tissue spatial segregation estimation. bioRxiv 470262, Cold Spring Harbor Laboratory.
Bayat, Amirhossein; Pace, Danielle F; Sekuboyina, Anjany; Payer, Christian; Stern, Darko; Urschler, Martin; Kirschke, Jan S; Menze, Bjoern H (2022). Anatomy-Aware Inference of the 3D Standing Spine Posture from 2D Radiographs. Tomography, 8(1):479-496.
Wagner, Johanna; Masek, Markus; Jacobs, Andrea; Soneson, Charlotte; Sivapatham, Sujana; Damond, Nicolas; de Souza, Natalie; Robinson, Mark D; Bodenmiller, Bernd (2022). Mass cytometric and transcriptomic profiling of epithelial-mesenchymal transitions in human mammary cell lines. Scientific Data, 9:44-60.
Paetzold, Johannes C; McGinnis, Julian; Shit, Suprosanna; Ezhov, Ivan; Büschl, Paul; Prabhakar, Chinmay; Todorov, Mihail I; Sekuboyina, Anjany; Kaissis, Georgios; Ertürk, Ali; Günnemann, Stephan; Menze, Bjoern (2022). Whole Brain Vessel Graphs: A Dataset and Benchmark for Graph Learning and Neuroscience (VesselGraph). ArXiv.org 2108.13233, Cornell University.
Mitamura, Yasutaka; Schulz, Daniel; Oro, Saskia; Li, Nick; Kolm, Isabel; Lang, Claudia; Ziadlou, Reihane; Tan, Ge; Bodenmiller, Bernd; Steiger, Peter; Marzano, Angelo; de Prost, Nicolas; Caudin, Olivier; Levesque, Mitchell; Stoffel, Corinne; Schmid-Grendelmeier, Peter; Maverakis, Emanual; Akdis, Cezmi A; Brüggen, Marie-Charlotte (2022). Cutaneous and systemic hyperinflammation drives maculopapular drug exanthema in severely ill COVID-19 patients. Allergy, 77(2):595-608.
Gafita, Andrei; Wang, Hui; Robertson, Andrew; Armstrong, Wesley R; Zaum, Raphael; Weber, Manuel; Yagubbayli, Farid; Kratochwil, Clemens; Grogan, Tristan R; Nguyen, Kathleen; Navarro, Fernando; Esfandiari, Rouzbeh; Rauscher, Isabel; Menze, Bjoern; Elashoff, David; Delpassand, Ebrahim S; Herrmann, Ken; Czernin, Johannes; Hofman, Michael S; Calais, Jeremie; Fendler, Wolfgang P; Eiber, Matthias (2022). Tumor Sink Effect in 68Ga-PSMA-11 PET: Myth or Reality? Journal of Nuclear Medicine, 63(2):226-232.
Jambeau, Melanie; Meyer, Kevin Daniel; Hruska-Plochan, Marian; Tabet, Ricardos; Lee, Chao-Zong; Ray-Soni, Ananya; Aguilar, Corey; Savage, Kitty; Mishra, Nibha; Cavegn, Nicole; Borter, Petra; Lin, Chun-Chia; Jansen-West, Karen; Jiang, Jay; Freyermuth, Fernande; Li, Nan; De Rossi, Pierre; Pérez-Berlanga, Manuela; et al; Maniecka, Zuzanna; Weber, Julien; Kankel, Mark W; Rushe, Mia; Hock, Christoph; Nitsch, Roger M; Cleveland, Don W; Montrasio, Fabio; Grimm, Jan; Polymenidou, Magdalini (2022). Comprehensive preclinical evaluation of human-derived anti-poly-GA antibodies in cellular and animal models of C9ORF72 disease. bioRxiv 475329, Cold Spring Harbor Laboratory.
Mächler, Leon; Ezhov, Ivan; Kofler, Florian; Shit, Suprosanna; Paetzold, Johannes C; Loehr, Timo; Zimmer, Claus; Wiestler, Benedikt; Menze, Bjoern H (2022). FedCostWAvg: A New Averaging for Better Federated Learning. In: Crimi, Alessandro; Bakas, Spyridon. Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. Cham: Springer, 383-391.
Sahadevan, Sonu; Pérez-Berlanga, Manuela; Polymenidou, Magdalini (2022). Identification of RNA–RBP Interactions in Subcellular Compartments by CLIP-Seq. In: Matějů, Daniel; Chao, Jeffrey A. The Integrated Stress Response - Methods and Protocols. New York: Springer, 305-323.
Lüdke, David; Amiranashvili, Tamaz; Ambellan, Felix; Ezhov, Ivan; Menze, Bjoern H; Zachow, Stefan (2022). Landmark-Free Statistical Shape Modeling Via Neural Flow Deformations. In: Wang, Linwei; Dou, Qi; Fletcher, Thomas P; Speidel, Stefanie; Liu, Shuo. Medical Image Computing and Computer Assisted Intervention : MICCAI 2022. Cham: Springer, 453-463.
Hoces, Daniel; Corak, Basak; Estrada Brull, Anna; Berent, Sara; Faccin, Erica; Moresi, Claudia; Keys, Tim; Joller, Nicole; Slack, Emma (2022). Microbiota colonization tunes the antigen threshold of microbiota-specific T cell activation in the gut. bioRxiv 501979, Cold Spring Harbor Laboratory.
Figueiredo, Alexandre R T; Özkaya, Özhan; Kümmerli, Rolf; Kramer, Jos (2022). Siderophores drive invasion dynamics in bacterial communities through their dual role as public good versus public bad. Ecology Letters, 25(1):138-150.
Shlesinger, Danielle; Hong, Kai-Lin; Shammas, Ghazal; Page, Nicolas; Sandu, Ioana; Agrafiotis, Andreas; Kreiner, Victor; Vincenti, Ilena; Wagner, Ingrid; Piccinno, Margot; Mariotte, Alexandre; Klimek, Bogna; Dizerens, Raphael; Manero-Carranza, Marcos; Kuhn, Raphael; Ehling, Roy; Frei, Lester; Khodaverdi, Keywan; Panetti, Camilla; Joller, Nicole; Oxenius, Annette; Merkler, Doron; Reddy, Sai T; Yermanos, Alexander; Fonta, Nicolas (2022). Single-cell immune repertoire sequencing of B and T cells in murine models of infection and autoimmunity. bioRxiv 479381, Cold Spring Harbor Laboratory.
Pérez-Berlanga, Manuela; Wiersma, Vera; Zbinden, Aurélie; De Vos, Laura; Wagner, Ulrich; Foglieni, Chiara; Mallona Gonzalez, Izaskun; Betz, Katharina M; Cléry, Antoine; Weber, Julien; Guo, Zhongning; Rigort, Ruben; De Rossi, Pierre; Manglunia, Ruchi; Tantardini, Elena; Sahadevan, Sonu; Stach, Oliver; Hruska-Plochan, Marian; Allain, Frederic H-T; Paganetti, Paolo; Polymenidou, Magdalini (2022). TDP-43 oligomerization and RNA binding are codependent but their loss elicits distinct pathologies. bioRxiv PPR49, Cold Spring Harbor Laboratory.
Iqbal, Jeffrey David; Krauthammer, Michael; Biller-Andorno, Nikola (2022). The Use and Ethics of Digital Twins in Medicine. Journal of Law, Medicine & Ethics, 50(3):583-596.
Kuett, Laura; Catena, Raúl; Özcan, Alaz; Plüss, Alex; Schraml, Peter; Moch, Holger; de Souza, Natalie; Bodenmiller, Bernd; Cancer Grand Challenges IMAXT Consortium (2022). Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment. Nature Cancer, 3(1):122-133.
Fujimoto, Koji; Nishio, Mizuho; Sugiyama, Osamu; Ichikawa, Kana; Cornelius, Joseph; Lithgow-Serrano, Oscar; Kanjirangat, Vani; Rinaldi, Fabio; Horvath, Aron N; Nooralahzadeh, Farhad; Krauthammer, Michael (2022). Approach for Named Entity Recognition and Case Identification Implemented by ZuKyo-JA Sub-team at the NTCIR-16 Real-MedNLP Task. In: NTCIR 16 Conference: Proceedings of the 16th NTCIR Conference on Evaluation of Information Access Technologies, Tokyo, Japan, 14 June 2022 - 17 June 2022, 322-329.
Heiliger, Lars; Sekuboyina, Anjany; Menze, Bjoern; Egger, Jan; Kleesiek, Jens (2022). Beyond Medical Imaging - A Review of Multimodal Deep Learning in Radiology. TechRxiv 19103432, University of Zurich.
Schwarz, Kyriakos; Pliego-Mendieta, Alicia; Mollaysa, Amina; Planas-Plaz, Lara; Pauli, Chantal; Allam, Ahmed; Krauthammer, Michael (2022). DDoS: A Graph Neural Network based Drug Synergy Prediction Algorithm. ArXiv.org 2210.00802, Cornell University.
Cornelius, Joseph; Lithgow-Serrano, Oscar; Kanjirangat, Vani; Rinaldi, Fabio; Fujimoto, Koji; Nishio, Mizuho; Sugiyama, Osamu; Ichikawa, Kana; Nooralahzadeh, Farhad; Horvath, Aron N; Krauthammer, Michael (2022). Leveraging Token-Based Concept Information and Data Augmentation in Few-Resource NER: ZuKyo-EN at the NTCIR-16 Real-MedNLP task. In: NTCIR 16 Conference: Proceedings of the 16th NTCIR Conference on Evaluation of Information Access Technologies, Tokyo, Japan, 14 June 2022 - 17 June 2022, NTCIR.
Windhager, Jonas. Multiplexed tissue image processing and spatial single-cell data integration. 2022, University of Zurich, Faculty of Science.
Bonvin, Raphaël; Buhmann, Joachim; Cotrini Jimenez, Carlos; Egger, Marcel; Geissler, Alexander; Krauthammer, Michael; Schirlo, Christian; Spiess, Christiane; Steurer, J; Vokinger, Kerstin N; Vogt, Julia. Neue Lernziele für das Medizinstudium erarbeitet. In: Neue Lernziele für das Medizinstudium erarbeitet, 2022, 98-101.
Liu, Hailing; Zhao, Yu; Yang, Fan; Lou, Xiaoying; Wu, Feng; Li, Hang; Xing, Xiaohan; Peng, Tingying; Menze, Bjoern; Huang, Junzhou; Zhang, Shujun; Han, Anjia; Yao, Jianhua; Fan, Xinjuan (2022). Preoperative Prediction of Lymph Node Metastasis in Colorectal Cancer with Deep Learning. BME Frontiers, 2022:9860179.
Pérez Berlanga, Manuela; Berlanga, Manuela Pérez. Roles of TDP-43 oligomerization and RNA binding in physiology and pathology. 2022, University of Zurich, Faculty of Science.
Kuett, Laura. Studying breast cancer invasion and metastasis with 2D and 3D imaging mass cytometry. 2022, University of Zurich, Faculty of Science.
Kofler, Florian; Ezhov, Ivan; Fidon, Lucas; Pirkl, Carolin M; Paetzold, Johannes C; Burian, Egon; Pati, Sarthak; El Husseini, Malek; Navarro, Fernando; Shit, Suprosanna; Kirschke, Jan; Bakas, Spyridon; Zimmer, Claus; Wiestler, Benedikt; Menze, Bjoern H (2021). Robust, Primitive, and Unsupervised Quality Estimation for Segmentation Ensembles. Frontiers in Neuroscience, 15:752780.
Kramer, Jos; Kümmerli, Rolf (2021). Losing out to improve group fitness. eLife, 10:e75243.
Zhylka, Andrey; Sollmann, Nico; Kofler, Florian; Radwan, Ahmed; De Luca, Alberto; Gempt, Jens; Wiestler, Benedikt; Menze, Bjoern; Krieg, Sandro M; Zimmer, Claus; Kirschke, Jan S; Sunaert, Stefan; Leemans, Alexander; Pluim, Josien P W (2021). Tracking the Corticospinal Tract in Patients With High-Grade Glioma: Clinical Evaluation of Multi-Level Fiber Tracking and Comparison to Conventional Deterministic Approaches. Frontiers in Oncology, 11:761169.
Endt, Sebastian; Pirkl, Carolin M; Verdun, Claudio M; Menze, Bjoern H; Menzel, Marion I (2021). Unmixing tissue compartments via deep learning T1-T2-relaxation correlation imaging. In: Seventeenth International Symposium on Medical Information Processing and Analysis, Campinas, Brazil, 17 November 2021 - 19 November 2021. SPIE, 120880P.
De Rossi, Pierre; Lewis, Amanda J; Furrer, Johanna; De Vos, Laura; Demeter, Tomas; Zbinden, Aurélie; Zhong, Weijia; Wiersma, Vera I; Scialo, Carlo; Weber, Julien; Guo, Zhongning; Scaramuzza, Stefano; Di Fabrizio, Marta; Böing, Carolin; Castaño‐Díez, Daniel; Al‐Amoudi, Ashraf; Pérez-Berlanga, Manuela; Lashley, Tammaryn; Stahlberg, Henning; Polymenidou, Magdalini (2021). FTLD‐TDP assemblies seed neoaggregates with subtype‐specific features via a prion‐like cascade. EMBO Reports, 22(12):e53877.
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Hu, Xiaobin; Ren, Wenqi; Yu, Kaicheng; Zhang, Kaihao; Cao, Xiaochun; Liu, Wei; Menze, Bjoern (2021). Pyramid Architecture Search for Real-Time Image Deblurring. In: 2021 IEEE/CVF International Conference on Computer Vision (ICCV), Montreal, QC, Canada, 10 October 2021 - 17 October 2021, IEEE.
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Guo, Rui; Hu, Xiaobin; Song, Haoming; Xu, Pengpeng; Xu, Haoping; Rominger, Axel; Lin, Xiaozhu; Menze, Bjoern; Li, Biao; Shi, Kuangyu (2021). Weakly supervised deep learning for determining the prognostic value of 18F-FDG PET/CT in extranodal natural killer/T cell lymphoma, nasal type. European Journal of Nuclear Medicine and Molecular Imaging, 48(10):3151-3161.
Niggli, Selina; Wechsler, Tobias; Kümmerli, Rolf (2021). Single-Cell Imaging Reveals That Staphylococcus aureus Is Highly Competitive Against Pseudomonas aeruginosa on Surfaces. Frontiers in Cellular and Infection Microbiology, 11:733991.
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Butaitė, Elena; Kramer, Jos; Kümmerli, Rolf (2021). Local adaptation, geographical distance and phylogenetic relatedness: Assessing the drivers of siderophore‐mediated social interactions in natural bacterial communities. Journal of Evolutionary Biology, 34(8):1266-1278.
Hiller, Helmut; Beachy, Dawn E; Lebowitz, Joseph J; Engler, Stefanie; Mason, Justin R; Miller, Douglas R; Kusmarteva, Irina; Jacobsen, Laura M; Posgai, Amanda L; Khoshbouei, Habibeh; Oram, Richard A; Schatz, Desmond A; Hattersley, Andrew T; Bodenmiller, Bernd; Atkinson, Mark A; Nick, Harry S; Wasserfall, Clive H (2021). Monogenic Diabetes and Integrated Stress Response Genes Display Altered Gene Expression in Type 1 Diabetes. Diabetes, 70(8):1885-1897.
Lu, Junyan; Cannizzaro, Ester; Meier-Abt, Fabienne; Scheinost, Sebastian; Bruch, Peter-Martin; Giles, Holly A R; Lütge, Almut; Hüllein, Jennifer; Wagner, Lena; Giacopelli, Brian; Nadeu, Ferran; Delgado, Julio; Campo, Elías; Mangolini, Maurizio; Ringshausen, Ingo; Böttcher, Martin; Mougiakakos, Dimitrios; Jacobs, Andrea; Bodenmiller, Bernd; Dietrich, Sascha; Oakes, Christopher C; Zenz, Thorsten; Huber, Wolfgang (2021). Multi-omics reveals clinically relevant proliferative drive associated with mTOR-MYC-OXPHOS activity in chronic lymphocytic leukemia. Nature cancer, 2(8):853-864.
Hoch, Tobias; Schulz, Daniel; Eling, Nils; Gómez, Julia Martínez; Levesque, Mitchell P; Bodenmiller, Bernd (2021). Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. bioRxiv 454093, Cold Spring Harbor Laboratory.
Emmenegger, Marc; De Cecco, Elena; Hruska‐Plochan, Marian; Eninger, Timo; Schneider, Matthias M; Barth, Melanie; Tantardini, Elena; de Rossi, Pierre; Bacioglu, Mehtap; Langston, Rebekah G; Kaganovich, Alice; Bengoa‐Vergniory, Nora; Gonzalez‐Guerra, Andrès; Avar, Merve; Heinzer, Daniel; Reimann, Regina; Häsler, Lisa M; Herling, Therese W; Matharu, Naunehal S; Landeck, Natalie; Luk, Kelvin; Melki, Ronald; Kahle, Philipp J; Hornemann, Simone; Knowles, Tuomas P J; Cookson, Mark R; Polymenidou, Magdalini; Jucker, Mathias; Aguzzi, Adriano (2021). LAG3 is not expressed in human and murine neurons and does not modulate α‐synucleinopathies. EMBO Molecular Medicine:e 14745.
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Bressan, Dario; Mulvey, Claire M; Qosaj, Fatime; Becker, Robert; Grimaldi, Flaminia; Coffey, Suvi; Vogl, Sara Lisa; Kuett, Laura; Catena, Raul; Dariush, Ali; Gonzalez-Fernandez, Carlos; Gonzalez-Solares, Eduardo A; Sa’d, Mohammad Al; Yoldaş, Aybüke Küpcü; Whitmarsh, Tristan; Falciatori, Ilaria; Watson, Spencer S; Joyce, Johanna A; Walton, Nicholas; Bodenmiller, Bernd; Harris, Owen; Hannon, Gregory J (2021). Exploration and analysis of molecularly annotated, 3D models of breast cancer at single-cell resolution using virtual reality. bioRxiv 448342, Cold Spring Harbor Laboratory.
Navarro, Fernando; Dapper, Hendrik; Asadpour, Rebecca; Knebel, Carolin; Spraker, Matthew B; Schwarze, Vincent; Schaub, Stephanie K; Mayr, Nina A; Specht, Katja; Woodruff, Henry C; Lambin, Philippe; Gersing, Alexandra S; Nyflot, Matthew J; Menze, Bjoern H; Combs, Stephanie E; Peeken, Jan C (2021). Development and External Validation of Deep-Learning-Based Tumor Grading Models in Soft-Tissue Sarcoma Patients Using MR Imaging. Cancers, 13(12):2866.
Navarro, Fernando; Watanabe, Christopher; Shit, Suprosanna; Sekuboyina, Anjany; Peeken, Jan C; Combs, Stephanie E; Menze, Bjoern H (2021). Evaluating the Robustness of Self-Supervised Learning in Medical Imaging. ArXiv.org 2105.06986, Cornell University.
Tognetti, Marco; Gabor, Attila; Yang, Mi; Cappelletti, Valentina; Windhager, Jonas; Rueda, Oscar M; Charmpi, Konstantina; Esmaeilishirazifard, Elham; Bruna, Alejandra; de Souza, Natalie; Caldas, Carlos; Beyer, Andreas; Picotti, Paola; Saez-Rodriguez, Julio; Bodenmiller, Bernd (2021). Deciphering the signaling network of breast cancer improves drug sensitivity prediction. Cell Systems, 12(5):401-418.e12.
González, Jaime; Salvador, Manuel; Özkaya, Özhan; Spick, Matt; Reid, Kate; Costa, Catia; Bailey, Melanie J; Avignone Rossa, Claudio; Kümmerli, Rolf; Jiménez, José I (2021). Loss of a pyoverdine secondary receptor in Pseudomonas aeruginosa results in a fitter strain suitable for population invasion. The ISME journal, 15(5):1330-1343.
Horvath, Izabela; Paetzold, Johannes C; Schoppe, Oliver; Al-Maskari, Rami; Ezhov, Ivan; Shit, Suprosanna; Li, Hongwei; Ertuerk, Ali; Menze, Bjoern (2021). METGAN: Generative Tumour Inpainting and Modality Synthesis in Light Sheet Microscopy. ArXiv.org 10993, Cornell University.
Li, Hongwei; Prasad, Rameshwara G N; Sekuboyina, Anjany; Niu, Chen; Bai, Siwei; Hemmert, Werner; Menze, Bjoern (2021). Micro-Ct Synthesis and Inner Ear Super Resolution via Generative Adversarial Networks and Bayesian Inference. In: 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI), Nice, France, 13 April 2021 - 16 April 2021. Institute of Electrical and Electronics Engineers, online.
Eling, Nils; Damond, Nicolas; Hoch, Tobias; Bodenmiller, Bernd (2021). Cytomapper: an R/bioconductor package for visualisation of highly multiplexed imaging data. Bioinformatics, 36(24):5706-5708.
Golbabaee, Mohammad; Buonincontri, Guido; Pirkl, Carolin M; Menzel, Marion I; Menze, Bjoern H; Davies, Mike; Gómez, Pedro A (2021). Compressive MRI quantification using convex spatiotemporal priors and deep encoder-decoder networks. Medical Image Analysis, 69:101945.
Jayakumar, Priyanikha; Thomas, Stephen A; Brown, Sam P; Kümmerli, Rolf (2021). Pseudomonas aeruginosa reaches collective decisions via transient segregation of quorum sensing activities across cells. bioRxiv 436499, Cold Spring Harbor Laboratory.
Kofler, Florian; Ezhov, Ivan; Isensee, Fabian; Balsiger, Fabian; Berger, Christoph; Koerner, Maximilian; Paetzold, Johannes C; Li, Hongwei; Shit, Suprosanna; McKinley, Richard; Spyridon, Bakas; Zimmer, Claus; Ankerst, Donna; Kirschke, Jan S; Wiestler, Benedikt; Menze, Bjoern (2021). Are we using appropriate segmentation metrics? Identifying correlates of human expert perception for CNN training beyond rolling the DICE coefficient. ArXiv.org 2103.06205, Cornell University.
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, 88:101828.
El‐Rewaidy, Hossam; Fahmy, Ahmed S; Pashakhanloo, Farhad; Cai, Xiaoying; Kucukseymen, Selcuk; Csecs, Ibolya; Neisius, Ulf; Haji‐Valizadeh, Hassan; Menze, Bjoern; Nezafat, Reza (2021). Multi‐domain convolutional neural network (MD‐CNN) for radial reconstruction of dynamic cardiac MRI. Magnetic Resonance in Medicine, 85(3):1195-1208.
Ramelyte, Egle; Tastanova, Aizhan; Balázs, Zsolt; Ignatova, Desislava; Turko, Patrick; Menzel, Ulrike; Guenova, Emmanuella; Beisel, Christian; Krauthammer, Michael; Levesque, Mitchell Paul; Dummer, Reinhard (2021). Oncolytic virotherapy-mediated anti-tumor response: a single-cell perspective. Cancer Cell, 39(3):394-406.e4.
Irmisch, Anja; Bonilla, Ximena; Chevrier, Stéphane; Lehmann, Kjong-Van; Singer, Franziska; Toussaint, Nora C; Esposito, Cinzia; Mena, Julien; Milani, Emanuela S; Casanova, Ruben; Stekhoven, Daniel J; Wegmann, Rebekka; Jacob, Francis; Sobottka-Brillout, Bettina; Goetze, Sandra; Kuipers, Jack; Sarabia del Castillo, Jacobo; Prummer, Michael; Tuncel, Mustafa A; Menzel, Ulrike; Jacobs, Andrea; Engler, Stefanie; Sivapatham, Sujana; Frei, Anja L; Gut, Gabriele; Ficek, Joanna; Miglino, Nicola; Aebersold, Rudolf; Bacac, Marina; Beerenwinkel, Niko; Moch, Holger; Beisel, Christian; Bodenmiller, Bernd; Dummer, Reinhard; Heinzelmann-Schwarz, Viola; Koelzer, Viktor H; Manz, Markus G; Pelkmans, Lucas; Snijder, Berend; Theocharides, Alexandre P A; Tolnay, Markus; Wicki, Andreas; Wollscheid, Bernd; Rätsch, Gunnar; Levesque, Mitchell Paul (2021). The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support. Cancer Cell, 39(3):288-293.
Giger, Johanna. Testing the evolutionary robustness of pyoverdine as a novel treatment against human opportunistic pathogens. 2021, University of Zurich, Faculty of Science.
Wennmann, Markus; Hielscher, Thomas; Kintzelé, Laurent; Menze, Bjoern H; Langs, Georg; Merz, Maximilian; Sauer, Sandra; Kauczor, Hans-Ulrich; Schlemmer, Heinz-Peter; Delorme, Stefan; Goldschmidt, Hartmut; Weinhold, Niels; Hillengass, Jens; Weber, Marc-André (2021). Analyzing Longitudinal wb-MRI Data and Clinical Course in a Cohort of Former Smoldering Multiple Myeloma Patients: Connections between MRI Findings and Clinical Progression Patterns. Cancers, 13(5):961.
Dong, Xingchen; Li, Hongwei; Jiang, Zhutong; Grünleitner, Theresa; Güler, İnci; Dong, Jie; Wang, Kun; Köhler, Michael H; Jakobi, Martin; Menze, Bjoern H; Yetisen, Ali K; Sharp, Ian D; Stier, Andreas V; Finley, Jonathan J; Koch, Alexander W (2021). 3D Deep Learning Enables Accurate Layer Mapping of 2D Materials. ACS Nano, 15(2):3139-3151.
Hu, Xiaobin; Zhao, Yu; Sekuboyina, Anjany; Menze, Bjoern (2021). Multi-Texture GAN: Exploring the Multi-Scale Texture Translation for Brain MR Images. ArXiv.org 2102.07225, Cornell University.
Alvarado-Cruz, Isabel; Mahmoud, Mariam; Khan, Mohammed; Zhao, Shilin; Oeck, Sebastian; Meas, Rithy; Clairmont, Kaylyn; Quintana, Victoria; Zhu, Ying; Porciuncula, Angelo; Wyatt, Hailey; Ma, Shuangge; Shyr, Yu; Kong, Yong; LoRusso, Patricia M; Laverty, Daniel; Nagel, Zachary D; Schalper, Kurt A; Krauthammer, Michael; Sweasy, Joann B (2021). Differential immunomodulatory effect of PARP inhibition in BRCA1 deficient and competent tumor cells. Biochemical Pharmacology, 184:114359.
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De Vargas Roditi, Laura; Jacobs, Andrea; Rueschoff, Jan H; Bankhead, Pete; Chevrier, Stéphane; Jackson, Hartland W; Hermanns, Thomas; Fankhauser, Christian Daniel; Poyet, Cédric; Chun, Felix; Rupp, Niels J; Tschaebunin, Alexandra; Bodenmiller, Bernd; Wild, Peter Johannes (2021). Single-Cell Proteomics Defines the Cellular Heterogeneity of Localized Prostate Cancer. bioRxiv 428046, Cold Spring Harbor Laboratory.
Chevrier, Stéphane; Zurbuchen, Yves; Cervia, Carlo; Adamo, Sarah; Raeber, Miro E; de Souza, Natalie; Sivapatham, Sujana; Jacobs, Andrea; Bachli, Esther; Rudiger, Alain; Stüssi-Helbling, Melina; Huber, Lars C; Schaer, Dominik J; Nilsson, Jakob; Boyman, Onur; Bodenmiller, Bernd (2021). A distinct innate immune signature marks progression from mild to severe COVID-19. Cell Reports Medicine, 2(1):100166.
Konrad, Sebastian F; Vanderlinden, Willem; Frederickx, Wout; Brouns, Tine; Menze, Björn H; De Feyter, Steven; Lipfert, Jan (2021). High-throughput AFM analysis reveals unwrapping pathways of H3 and CENP-A nucleosomes. Nanoscale, 13(10):5435-5447.
Li, Hongwei; Xue, Fei-Fei; Chaitanya, Krishna; Luo, Shengda; Ezhov, Ivan; Wiestler, Benedikt; Zhang, Jianguo; Menze, Bjoern (2021). Imbalance-Aware Self-supervised Learning for 3D Radiomic Representations. In: de Buijne, Marleen; Cotin, Stéphane; Speidel, Stefanie; Zhen, Yefeng; Essert, Caroline. Medical Immage Computing and Computer Assisted Intervention - MICCAI 2021. Strasbourg: Springer, 36-46.
Shit, Suprosanna; Das, Dhritiman; Ezhov, Ivan; Paetzold, Johannes C; Sanches, Augusto F; Thuerey, Nils; Menze, Bjoern H (2021). Velocity-To-Pressure (V2P) - Net: Inferring Relative Pressures from Time-Varying 3D Fluid Flow Velocities. In: Feragen, Aasa; Sommer, Stefan; Schnabel, J; Nielsen, Mads. Information Processing in Medical Imaging. Cham: Springer, 545-558.
Schwarz, Kyriakos; Allam, Ahmed; Perez Gonzalez, Nicolas Andres; Krauthammer, Michael (2021). AttentionDDI: Siamese attention‑based deep learning method for drug–drug interaction predictions. BMC Bioinformatics, 22(1):412.
Shit, Suprosanna; Ezhov, Ivan; Paetzold, Johannes C; Menze, Bjoern (2021). Aν-Net: Automatic Detection and Segmentation of Aneurysm. In: Hennemuth, A. Cerebral Aneurysm Detection and Analysis. Cham: Springer, 51-57.
Ma, Jiechao; Li, Xiang; Li, Hongwei; Wang, Ruixuan; Menze, Bjoern; Zheng, Wei-Shi (2021). Cross-View Relation Networks for Mammogram Mass Detection. In: 2020 25th International Conference on Pattern Recognition (ICPR), Milan, Italy, 10 January 2021 - 15 January 2021. Institute of Electrical and Electronics Engineers, 8632-8638.
Mridha, Subham. Ecology and Evolution of Bacterial Social Behaviours in Phenotypically Heterogenous Populations. 2021, University of Zurich, Faculty of Science.
Niggli, Selina. Ecology and Evolution of Interspecies Interactions between Pseudomonas aeruginosa and Staphylococcus aureus. 2021, University of Zurich, Faculty of Science.
Fischer, Jana Raja. High-dimensional profiling of the breast cancer microarchitecture. 2021, University of Zurich, Faculty of Science.
Tietscher, Sandra. Single-cell profiling of the tumor immune microenvironment of primary and metastatic human breast cancer. 2021, University of Zurich, Faculty of Science.
Figueiredo, Alexandre R T. The Ecology and Evolution of Bacterial Social Interactions and How They Shape Microbial Communities and Interactions with Hosts. 2021, University of Zurich, Faculty of Science.
Wiestler, Benedikt; Menze, Bjoern (2020). Deep learning for medical image analysis: a brief introduction. Neuro-Oncology Advances, 2(Supplement):iv35-iv41.
Tetteh, Giles; Efremov, Velizar; Forkert, Nils D; Schneider, Matthias; Kirschke, Jan; Weber, Bruno; Zimmer, Claus; Piraud, Marie; Menze, Björn H (2020). DeepVesselNet: Vessel Segmentation, Centerline Prediction, and Bifurcation Detection in 3-D Angiographic Volumes. Frontiers in Neuroscience, 14:592352.
Kinkead, Laura; Allam, Ahmed; Krauthammer, Michael (2020). AutoDiscern: rating the quality of online health information with hierarchical encoder attention-based neural networks. BMC Medical Informatics and Decision Making, 20:104.
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