DQBM Publications 2022 Bernd Bodenmiller CSV EndNote BibTeX XML Export Wild, Sophia A; Cannell, Ian G; Nicholls, Ashley; Kania, Katarzyn; Bressan, Dario; Hannon, Gregory J; Sawicka, Kirsty; Bodenmiller, Bernd (2022). Clonal transcriptomics identifies mechanisms of chemoresistance and empowers rational design of combination therapies. eLife, 11:e80981. Wang, Jian; Weiss, Tobias; Neidert, Marian C; Toussaint, Nora C; Naghavian, Reza; Moreno Sellés, Carla; Foege, Magdalena; Tomas Ojer, Paula; Medici, Gioele; Jelcic, Ivan; Schulz, Daniel; Rushing, Elisabeth; Dettwiler, Susanne; Schrörs, Barbara; Shin, Joo Heon; McKay, Ron; Wu, Catherine J; Lutterotti, Andreas; Sospedra, Mireia; Moch, Holger; Greiner, Erich F; Bodenmiller, Bernd; Regli, Luca; Weller, Michael; Roth, Patrick; Martin, Roland (2022). Vaccination with designed neopeptides induces intratumoral, cross-reactive CD4+ T cell responses in glioblastoma. Clinical Cancer Research, 28(24):5368-5382. Funnell, Tyler; Bodenmiller, Bernd (2022). Single-cell genomic variation induced by mutational processes in cancer. Nature, 612(7938):106-115. Martinelli, Adriano Luca; Wagner, Johanna; Bodenmiller, Bernd; Rapsomaniki, Maria Anna (2022). scQUEST: Quantifying tumor ecosystem heterogeneity from mass or flow cytometry data. STAR Protocols, 3(3):101578. Taeschler, Patrick; Adamo, Sarah; Deng, Yun; Cervia, Carlo; Zurbuchen, Yves; Chevrier, Stéphane; Raeber, Miro E; Hasler, Sara; Bächli, Esther; Rudiger, Alain; Stüssi-Helbling, Melina; Huber, Lars C; Bodenmiller, Bernd; Boyman, Onur; Nilsson, Jakob (2022). T-cell recovery and evidence of persistent immune activation 12 months after severe COVID-19. Allergy, 77(8):2468-2481. 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. 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. 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. 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, University of Zurich. 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. Bost, Pierre; Schulz, Daniel; Engler, Stefanie; Wasserfall, Clive H; Bodenmiller, Bernd (2022). Optimizing multiplexed imaging experimental design through tissue spatial segregation estimation. bioRxiv 470262, University of Zurich. 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. 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. 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. Nicole Joller Shlesinger, Danielle; Hong, Kai-Lin; Shammas, Ghazal; Page, Nicolas; Sandu, Ioana; Agrafiotis, Andreas; Kreiner, Victor; Fonta, Nicolas; 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 (2022). Single-cell immune repertoire sequencing of B and T cells in murine models of infection and autoimmunity. Genes and immunity:183-195. 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. 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. Panetti, Camilla; Kao, Kung‐Chi; Joller, Nicole (2022). Dampening antiviral immunity can protect the host. FEBS Journal, 289(3):634-646. 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, University of Zurich. 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, University of Zurich. Michael Krauthammer Garaiman, Alexandru; Nooralahzadeh, Farhad; Mihai, Carina; Gonzalez, Nicolas Perez; Gkikopoulos, Nikitas; Becker, Mike Oliver; Distler, Oliver; Krauthammer, Michael; Maurer, Britta (2022). Vision transformer assisting rheumatologists in screening for capillaroscopy changes in systemic sclerosis: an artificial intelligence model. Rheumatology:Epub ahead of print. Restivo, Gaetana; Tastanova, Aizhan; Balázs, Zsolt; Panebianco, Federica; Diepenbruck, Maren; Ercan, Caner; Preca, Bodgan-T; Hafner, Jürg; Weber, Walter P; Kurzeder, Christian; Vetter, Marcus; Soysal, Simone Münst; Beisel, Christian; Bentires-Alj, Mohamed; Piscuoglio, Salvatore; Krauthammer, Michael; Levesque, Mitchell P (2022). Live slow-frozen human tumor tissues viable for 2D, 3D, ex vivo cultures and single-cell RNAseq. Communications Biology, 5:1144. Eichhoff, Ossia M; Stoffel, Corinne Isabelle; Käsler, Jan; Briker, Luzia; Turko, Patrick; Karsai, Gergely; Zila, Nina; Paulitschke, Verena; Cheng, Phil F; Leitner, Alexander; Bileck, Andrea; Zamboni, Nicola; Irmisch, Anja; Balázs, Zsolt; Tastanova, Aizhan; Pascoal, Susana; Johansen, Pål; Wegmann, Rebekka; Mena, Julien; Othman, Alaa; Viswanathan, Vasanthi S; Wenzina, Judith; Aloia, Andrea; Saltari, Annalisa; Dzung, Andreas; Krauthammer, Michael; Schreiber, Stuart L; Hornemann, Thorsten; Distel, Martin; Snijder, Berend; Dummer, R; Levesque, Mitchell (2022). ROS induction as a strategy to target persister cancer cells with low metabolic activity in NRAS mutated melanoma. bioRxiv 512839, University of Zurich. Schwarz, Kyriakos; Trejo Banos, Daniel; Rathmes, Giulia; Krauthammer, Michael (2022). Drug prescription clusters in the UK Biobank: An assessment of drug-drug interactions and patient outcomes in a large patient cohort. arXiv.org 2207.08665, University of Zurich. 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. 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. 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 2204.11351, University of Zurich. 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. 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. 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. 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. Schwarz, Kyriakos; Pliego-Mendieta, Alicia; Planas-Plaz, Lara; Pauli, Chantal; Allam, Ahmed; Krauthammer, Michael (2022). DDoS: A Graph Neural Network based Drug Synergy Prediction Algorithm. arXiv.org 2210.00802, University of Zurich. 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. 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. Rolf Kümmerli Kümmerli, Rolf (2022). Iron acquisition strategies in pseudomonads: mechanisms, ecology, and evolution. Biometals:Epub ahead of print. Jayakumar, Priyanikha; Thomas, Stephen A; Brown, Sam P; Kümmerli, Rolf (2022). Collective decision-making in Pseudomonas aeruginosa involves transient segregation of quorum-sensing activities across cells. Current Biology, 32(24):5250-5261.e6. Mridha, Subham; Kümmerli, Rolf (2022). Coordination of siderophore gene expression among clonal cells of the bacterium Pseudomonas aeruginosa. Communications Biology, 5(1):545. Jayakumar, Priyanikha; Figueiredo, Alexandre R T; Kümmerli, Rolf (2022). Evolution of Quorum Sensing in <i>Pseudomonas aeruginosa</i> Can Occur via Loss of Function and Regulon Modulation. mSystems, 7(5):e0035422. Schmitz, Désirée A; Allen, Richard C; Kümmerli, Rolf (2022). Negative interactions and virulence differences drive the dynamics in multispecies bacterial infections. bioRxiv 503476, University of Zurich. 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. 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, University of Zurich. 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. 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. Bjoern Menze 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; Boeckh-Behrens, Tobias; Berndt, Maria; Ikenberg, Benno; Wiestler, Benedikt; Kirschke, Jan S (2022). ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset. Scientific Data, 9(1):762. Bhatia, Harsharan Singh; Brunner, Andreas-David; Öztürk, Furkan; Kapoor, Saketh; Rong, Zhouyi; Mai, Hongcheng; Thielert, Marvin; Ali, Mayar; Al-Maskari, Rami; Paetzold, Johannes Christian; Kofler, Florian; Todorov, Mihail Ivilinov; Molbay, Muge; Kolabas, Zeynep Ilgin; Negwer, Moritz; Hoeher, Luciano; Steinke, Hanno; Dima, Alina; Gupta, Basavdatta; Kaltenecker, Doris; Caliskan, Özüm Sehnaz; Brandt, Daniel; Krahmer, Natalie; Müller, Stephan; Lichtenthaler, Stefan Frieder; Hellal, Farida; Bechmann, Ingo; Menze, Bjoern; Theis, Fabian; Mann, Matthias (2022). Spatial proteomics in three-dimensional intact specimens. Cell, 185(26):5040-5058.e19. Hu, Xiaobin; Ren, Wenqi; Yang, Jiaolong; Cao, Xiaochun; Wipf, David P; Menze, Bjoern; Tong, Xin; Zha, Hongbin (2022). Face Restoration via Plug-and-Play 3D Facial Priors. IEEE transactions on software engineering, 44(12):8910-8926. Pati, Sarthak; Baid, Ujjwal; Edwards, Brandon; Sheller, Micah J; Foley, Patrick; Anthony Reina, G; Thakur, Siddhesh; Sako, Chiharu; Bilello, Michel; Davatzikos, Christos; Martin, Jason; Shah, Prashant; Menze, Bjoern; Bakas, Spyridon (2022). The federated tumor segmentation (FeTS) tool: an open-source solution to further solid tumor research. Physics in Medicine and Biology, 67(20):204002. 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). Application of machine learning to pretherapeutically estimate dosimetry in men with advanced prostate cancer treated with 177Lu-PSMA I&T therapy. European Journal of Nuclear Medicine and Molecular Imaging, 49(12):4064-4072. Neubauer, Antonia; Li, Hongwei Bran; Wendt, Jil; Schmitz-Koep, Benita; Menegaux, Aurore; Schinz, David; Menze, Bjoern; Zimmer, Claus; Sorg, Christian; Hedderich, Dennis M (2022). Efficient Claustrum Segmentation in T2-weighted Neonatal Brain MRI Using Transfer Learning from Adult Scans. Clinical Neuroradiology, 32(3):665-676. Mehta, Raghav; Menze, Bjoern H; et al (2022). QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results. arXiv.org 2112.1007, University of Zurich. Wittmann, Bastian; Navarro, Fernando; Shit, Suprosanna; Menze, Bjoern H (2022). Focused Decoding Enables 3D Anatomical Detection by Transformers. arXiv.org 2207.10774, University of Zurich. Sudre, Carole H; Ezhov, Ivan; Kofler, Florian; Menze, Bjoern H; et al (2022). Where is VALDO? VAscular Lesions Detection and segmentatiOn challenge at MICCAI 2021. arXiv.org 2208.07167, University of Zurich. Shit, Suprosanna; Zimmermann, Judith; Ezhov, Ivan; Paetzold, Johannes C; Sanches, Augusto F; Pirkl, Carolin; Menze, Bjoern H (2022). SRflow: Deep learning based super-resolution of 4D-flow MRI data. Frontiers in Artificial Intelligence, 5:928181. Ezhov, Ivan; Zimmer, Lucas; Menze, Bjoern; et al (2022). A for-loop is all you need. For solving the inverse problem in the case of personalized tumor growth modeling. arXiv.org 2205.04550, University of Zurich. Menten, Martin J; Paetzold, Johannes C; Dima, Alina; Menze, Bjoern H; Knierim, B; Rueckert, Daniel (2022). Physiology-based simulation of the retinal vasculature enables annotation-free segmentation of OCT angiographs. arXiv.org 2207.11102, University of Zurich. Ezhov, Ivan; Scibilia, Kevin; Franitza, Katharina; Steinbauer, Felix; Shit, Suprosanna; Zimmer, Lucas; Lipková, Jana; Kofler, Florian; Paetzold, Johannes C; Canalini, Luca; Waldmannstetter, Diana; Menten, Martin J; Metz, Marie; Wiestler, Benedikt; Menze, Bjoern H (2022). Learn-Morph-Infer: a new way of solving the inverse problem for brain tumor modeling. arXiv.org 2111.04090, University of Zurich. 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, University of Zurich. 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, University of Zurich. Maier-Hein, Lena; et al; Menze, Bjoern (2022). Metrics reloaded: Pitfalls and recommendations for image analysis validation. arXiv.org 2206.01653, University of Zurich. 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 Juli 2022. MLResearch Press, 1-13. 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. 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 : Cold Spring Harbor Laboratory 22276371, University of Zurich. 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, University of Zurich. 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, University of Zurich. Ezhov, Ivan; Mot, Tudor; Shit, Suprosanna; Lipková, Jana; Paetzold, Johannes C; Kofler, Florian; Pellegrini, Chantal; Kollovieh, Marcel; Navarro, Fernando; Li, Hongwei; Metz, Marie; Wiestler, Benedikt; Menze, Bjoern (2022). Geometry-aware neural solver for fast Bayesian calibration of brain tumor models. IEEE Transactions on Medical Imaging, 41(5):1269-1278. 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. 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. 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. 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. 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. 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, University of Zurich. 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, University of Zurich. 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. 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, University of Zurich. 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. 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. 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. 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, University of Zurich. 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. 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. 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. 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. 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. Magdalini Polymenidou Jambeau, Melanie; Meyer, Kevin D; Hruska-Plochan, Marian; et al; Cavegn, Nicole; Borter, Petra; De Rossi, Pierre; Pérez-Berlanga, Manuela; Maniecka, Zuzanna; Weber, Julien; Hock, Christoph; Nitsch, Roger M; Petrucelli, Leonard; Gendron, Tania F; Montrasio, Fabio; Grimm, Jan; Polymenidou, Magdalini (2022). Comprehensive evaluation of human-derived anti-poly-GA antibodies in cellular and animal models of C9orf72 disease. Proceedings of the National Academy of Sciences of the United States of America, 119(49):e2123487119. Avar, Merve; Heinzer, Daniel; Thackray, Alana M; Liu, Yingjun; Hruska‐Plochan, Marian; Sellitto, Stefano; Schaper, Elke; Pease, Daniel P; Yin, Jiang‐An; Lakkaraju, Asvin KK; Emmenegger, Marc; Losa, Marco; Chincisan, Andra; Hornemann, Simone; Polymenidou, Magdalini; Bujdoso, Raymond; Aguzzi, Adriano (2022). An arrayed genome‐wide perturbation screen identifies the ribonucleoprotein Hnrnpk as rate‐limiting for prion propagation. EMBO Journal Online, 41(23):e112338. Wiersma, Vera I; Rigort, Ruben; Polymenidou, Magdalini (2022). Tau: a phase in the crowd. EMBO Journal Online, 41:e111425. 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, University of Zurich. 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. 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, University of Zurich. 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, University of Zurich. 2021 Bernd Bodenmiller CSV EndNote BibTeX XML Export Windhager, Jonas; Bodenmiller, Bernd; Eling, Nils (2021). An end-to-end workflow for multiplexed image processing and analysis. bioRxiv 468357, University of Zurich. Gabor, Attila; Tognetti, Marco; Driessen, Alice; Tanevski, Jovan; et al; Bodenmiller, Bernd; Saez‐Rodriguez, Julio (2021). Cell‐to‐cell and type‐to‐type heterogeneity of signaling networks: insights from the crowd. Molecular Systems Biology, 17(10):e10402. Adamo, Sarah; Chevrier, Stéphane; Cervia, Carlo; Zurbuchen, Yves; Raeber, Miro E; Yang, Liliane; Sivapatham, Sujana; Jacobs, Andrea; Baechli, Esther; Rudiger, Alain; Stüssi‐Helbling, Melina; Huber, Lars C; Schaer, Dominik J; Bodenmiller, Bernd; Boyman, Onur; Nilsson, Jakob (2021). Profound dysregulation of T cell homeostasis and function in patients with severe COVID‐19. Allergy, 76(9):2866-2881. 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, University of Zurich. 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, University of Zurich. 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. 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. 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. Alon, Shahar; Goodwin, Daniel R; Sinha, Anubhav; Wassie, Asmamaw T; Chen, Fei; et al; IMAXT Consortium; Bodenmiller, Bernd; Kuett, L; Tietscher, S; Windhager, Jonas (2021). Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems. Science, 371(6528):eaax2656. 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, University of Zurich. 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. Nicole Joller CSV EndNote BibTeX XML Export Borsa, Mariana; Barandun, Niculò; Gräbnitz, Fabienne; Barnstorf, Isabel; Baumann, Nicolas S; Pallmer, Katharina; Baumann, Samira; Stark, Dominique; Balaz, Miroslav; Oetiker, Nathalie; Wagen, Franziska; Wolfrum, Christian; Simon, Anna Katharina; Joller, Nicole; Barral, Yves; Spörri, Roman; Oxenius, Annette (2021). Asymmetric cell division shapes naive and virtual memory T-cell immunity during ageing. Nature Communications, 12:2715. Michael Krauthammer CSV EndNote BibTeX XML Export Allam, Ahmed; Feuerriegel, Stefan; Rebhan, Michael; Krauthammer, Michael (2021). Analyzing Patient Trajectories With Artificial Intelligence. Journal of Medical Internet Research, 23(12):e29812. Rathmes, Giulia; Krauthammer, Michael (2021). Künstliche Intelligenz in der Medizin : Chancen und Risiken der KI. Hausarzt Praxis, 16(11):6-10. Thouvenin, Florent; Christen, Markus; Bernstein, Abraham; Braun Binder, Nadja; Burri, Thomas; Donnay, Karsten; Jäger, Lena A; Jaffé, Mariela; Krauthammer, Michael; Lohmann, Melinda; Mätzener, Anna; Mützel, Sophie; Obrecht, Liliane; Ritter, Nicole; Spielkamp, Matthias; Volz, Stephanie (2021). Positionspapier: Ein Rechtsrahmen für Künstliche Intelligenz. In: Workshop of the DSI (Digital Society Initiative) Strategy Lab, Balsthal, 26 August 2021 - 28 August 2021. Digital Society Initiative, 1-7. Montalban-Arques, Ana; Katkeviciute, Egle; Busenhart, Philipp; Bircher, Anna; Wirbel, Jakob; Zeller, Georg; Morsy, Yasser; Borsig, Lubor; Glaus Garzon, Jesus Francisco; Müller, Anne; Arnold, Isabelle C; Artola-Borán, Mariela; Krauthammer, Michael; Sintsova, Anna; Zamboni, Nicola; Leventhal, Gabriel E; Berchtold, Laura; de Wouters, Tomas; Rogler, Gerhard; Baebler, Katharina; Schwarzfischer, Marlene; Hering, Larissa; Olivares-Rivas, Ivan; Atrott, Kirstin; Gottier, Claudia; Lang, Silvia; Boyman, Onur; Fritsch, Ralph M; Manz, Markus G; Spalinger, Marianne R; Scharl, Michael (2021). Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors. Cell Host & Microbe, 29(10):1573-1588.e7. Marquart, Kim F; Allam, Ahmed; Janjuha, Sharan; Sintsova, Anna; Villiger, Lukas; Frey, Nina; Krauthammer, Michael; Schwank, Gerald (2021). Predicting base editing outcomes with an attention-based deep learning algorithm trained on high-throughput target library screens. Nature Communications, 12:5114. Maibach, Martina A; Allam, Ahmed; Hilty, Matthias P; Perez Gonzalez, Nicolas A; Buehler, Philipp K; Wendel Garcia, Pedro D; Brugger, Silvio D; Ganter, Christoph C; CoViD-19 ICU-Research Group Zurich; RISC-19-ICU Investigators; Krauthammer, Michael; Schuepbach, Reto A; Bartussek, Jan (2021). How to Synchronize Longitudinal Patient Data With the Underlying Disease Progression: A Pilot Study Using the Biomarker CRP for Timing COVID-19. Frontiers in Medicine, 8:607594. Tastanova, Aizhan; Ramelyte, Egle; Balázs, Zsolt; Menzel, Ulrike; Beisel, Christian; Krauthammer, Michael; Dummer, Reinhard; Levesque, Mitchell Paul (2021). Collection and preprocessing of fine needle aspirate patient samples for single cell profiling and data analysis. STAR Protocols, 2(2):100581. 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. 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. 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. Nooralahzadeh, Farhad; Perez Gonzalez, Nicolas; Frauenfelder, Thomas; Fujimoto, Koji; Krauthammer, Michael (2021). Progressive Transformer-Based Generation of Radiology Reports. In: Empirical Methods in Natural Language Processing (EMNLP), Punta Cana, 7 November 2021 - 11 November 2021. ACL Anthology, 2824-2832. Rolf Kümmerli CSV EndNote BibTeX XML Export Kramer, Jos; Kümmerli, Rolf (2021). Losing out to improve group fitness. eLife, 10:e75243. Figueiredo, Alexandre R T; Wagner, Andreas; Kümmerli, Rolf (2021). Ecology drives the evolution of diverse social strategies in Pseudomonas aeruginosa. Molecular Ecology, 30(20):5214-5228. 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. Niggli, Selina; Poveda, Lucy; Grossmann, Jonas; Kümmerli, Rolf (2021). Rapid and strain-specific resistance evolution of Staphylococcus aureus against inhibitory molecules secreted by Pseudomonas aeruginosa. bioRxiv 455797, University of Zurich. 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. 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. 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, University of Zurich. Bjoern Menze CSV EndNote BibTeX XML Export 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. 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. Baheti, Bhakti; Waldmannstetter, Diana; Chakrabarty, Satrajit; Akbari, Mohammad; Bilello, Michel; Wiestler, Benedikt; Schwarting, Julian; Calabrese, Evan; Jeffrey, Rudie; Abidi, Syed; Mousa, Mina; Villanueva-Meyer, Javier; Marcus, Daniel S; Davathikos, Christos; Sotiras, Aristeidis; Menze, Bjoern H; Bakas, Spyridon (2021). The Brain Tumor Sequence Registration Challenge: Establishing Correspondence between Pre-Operative and Follow-up MRI scans of diffuse glioma patients. arXiv.org 2112.06979, University of Zurich. Campello, Victor M; Gkontra, Polyxeni; Izquierdo, Cristian; Martin-Isla, Carlos; et al; Menze, Bjoern (2021). Multi-Centre, Multi-Vendor and Multi-Disease Cardiac Segmentation: The M&Ms Challenge. IEEE Transactions on Medical Imaging, 40(12):3543-3554. de la Rosa, Ezequiel; Sima, Diana M; Menze, Bjoern; Kirschke, Jan S; Robben, David (2021). AIFNet: Automatic vascular function estimation for perfusion analysis using deep learning. Medical Image Analysis, 74:102211. Liebl, Hans; Schinz, David; Sekuboyina, Anjany; Malagutti, Luca; Löffler, Maximilian T; Bayat, Amirhossein; El Husseini, Malek; Tetteh, Giles; Grau, Katharina; Niederreiter, Eva; Baum, Thomas; Wiestler, Benedikt; Menze, Bjoern; Braren, Rickmer; Zimmer, Claus; Kirschke, Jan S (2021). A computed tomography vertebral segmentation dataset with anatomical variations and multi-vendor scanner data. Scientific Data, 8:284. Bhatia, Harsharan Singh; Brunner, Andreas-David; Rong, Zhouyi; Mai, Hongcheng; Thielert, Marvin; Al-Maskari, Rami; Paetzold, Johannes Christian; Kofler, Florian; Todorov, Mihail Ivilinov; Ali, Mayar; Molbay, Muge; Kolabas, Zeynep Ilgin; Kaltenecker, Doris; Müller, Stephan; Lichtenthaler, Stefan F; Menze, Bjoern H; Theis, Fabian J; Mann, Matthias; Ertürk, Ali (2021). Proteomics of spatially identified tissues in whole organs. bioRxiv 466753, University of Zurich. Pirkl, Carolin M; Nunez-Gonzalez, Laura; Kofler, Florian; Endt, Sebastian; Grundl, Lioba; Golbabaee, Mohammad; Gómez, Pedro A; Cencini, Matteo; Buonincontri, Guido; Schulte, Rolf F; Smits, Marion; Wiestler, Benedikt; Menze, Bjoern H; Menzel, Marion I; Hernandez-Tamames, Juan A (2021). Accelerated 3D whole-brain T1, T2, and proton density mapping: feasibility for clinical glioma MR imaging. Neuroradiology, 63(11):1831-1851. Tetteh, Giles; Navarro, Fernando; Paetzold, Johannes C; Kirschke, Jan S; Zimmer, Claus; Menze, Bjoern H (2021). A Deep Learning Approach to Predicting Collateral Flow in Stroke Patients Using Radiomic Features from Perfusion Images. arXiv.org 2110.12508, University of Zurich. 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. Shit, Suprosanna; et al; Menze, Bjoern (2021). Semi-Implicit Neural Solver for Time-dependent Partial Differential Equations. arXiv.org 2109.01467, University of Zurich. Pati, Sarthak; Thakur, Siddhesh; Bhalerao, Megh; Thermos, Spyridon; Baid, Ujjwal; Gotkowski, Karol; Gonzalez, Camila; Güley, Orhun; Hamamci, Ibrahim Ethem; Er, Sezgin; Grenko, Caleb; Brandon, Edwards; Sheller, Micah; Agraz, Jose; Baheti, Bhakti; Bashyam, Vishnu; Sharma, Parth; Haghighi, Babak; Gastounioti, Aimilia; Bergman, Mark; Anirban, Mukhopadhyay; Sotirios A., Tsaftaris; Menze, Bjoern; Kontos, Despina; Davatzikos, Christos; Bakas, Spyridon (2021). GaNDLF: A Generally Nuanced Deep Learning Framework for Scalable End-to-End Clinical Workflows in Medical Imaging. arXiv.org 2103.01006, University of Zurich. 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. Timmins, Kimberley M; van der Schaaf, Irene C; Bennink, Edwin; Ruigrok, Ynte M; An, Xingle; Baumgartner, Michael; Bourdon, Pascal; De Feo, Riccardo; Noto, Tommaso Di; Dubost, Florian; Fava-Sanches, Augusto; Feng, Xue; Giroud, Corentin; Group, Inteneural; Hu, Minghui; Jaeger, Paul F; Kaiponen, Juhana; Klimont, Michał; Li, Yuexiang; Li, Hongwei; Lin, Yi; Loehr, Timo; Ma, Jun; Maier-Hein, Klaus H; Marie, Guillaume; Menze, Bjoern; Richiardi, Jonas; Rjiba, Saifeddine; Shah, Dhaval; Shit, Suprosanna (2021). Comparing methods of detecting and segmenting unruptured intracranial aneurysms on TOF-MRAS: The ADAM challenge. NeuroImage, 238:118216. Payette, Kelly; de Dumast, Priscille; Kebiri, Hamza; Ezhov, Ivan; Paetzold, Johannes C; Shit, Suprosanna; Iqbal, Asim; Khan, Romesa; Kottke, Raimund; Grehten, Patrice; Ji, Hui; Lanczi, Levente; Nagy, Marianna; Beresova, Monika; Nguyen, Thi Dao; Natalucci, Giancarlo; Karayannis, Theofanis; Menze, Bjoern; Bach Cuadra, Meritxell; Jakab, András (2021). An automatic multi-tissue human fetal brain segmentation benchmark using the Fetal Tissue Annotation Dataset. Scientific Data, 8(1):167-181. 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, University of Zurich. 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, University of Zurich. 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, IEEE. 1 2 Magdalini Polymenidou CSV EndNote BibTeX XML Export 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. Scekic-Zahirovic, Jelena; Sanjuan-Ruiz, Inmaculada; Kan, Vanessa; Megat, Salim; De Rossi, Pierre; Dieterlé, Stéphane; Cassel, Raphaelle; Jamet, Marguerite; Kessler, Pascal; Wiesner, Diana; Tzeplaeff, Laura; Demais, Valérie; Sahadevan, Sonu; Hembach, Katharina M; Muller, Hans-Peter; Picchiarelli, Gina; Mishra, Nibha; Antonucci, Stefano; Dirrig-Grosch, Sylvie; Kassubek, Jan; Rasche, Volker; Ludolph, Albert; Boutillier, Anne-Laurence; Roselli, Francesco; Polymenidou, Magdalini; Lagier-Tourenne, Clotilde; Liebscher, Sabine; Dupuis, Luc (2021). Cytoplasmic FUS triggers early behavioral alterations linked to cortical neuronal hyperactivity and inhibitory synaptic defects. Nature Communications, 12:3028. Sahadevan, Sonu; Hembach, Katharina M; Tantardini, Elena; Pérez-Berlanga, Manuela; Hruska-Plochan, Marian; Megat, Salim; Weber, Julien; Schwarz, Petra; Dupuis, Luc; Robinson, Mark D; De Rossi, Pierre; Polymenidou, Magdalini (2021). Synaptic FUS accumulation triggers early misregulation of synaptic RNAs in a mouse model of ALS. Nature Communications, 12(1):3027. Wiersma, Vera I; Polymenidou, Magdalini (2021). Sharing is caring: The benefits of distributing protein aggregates among microglial networks. Neuron, 109(20):3228-3230. 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. 2020 Bernd Bodenmiller CSV EndNote BibTeX XML Export Zanotelli, Vito R T; Leutenegger, Matthias; Lun, Xiao-Kang; Georgi, Fanny; de Souza, Natalie; Bodenmiller, Bernd (2020). A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids. Molecular Systems Biology, 16:e9798. Wade, James D; Lun, Xiao-Kang; Bodenmiller, Bernd; Voit, Eberhard O (2020). Multidimensional single-cell modeling of cellular signaling. bioRxiv 383711, University of Zurich. Tortola, Luigi; Jacobs, Andrea; Pohlmeier, Lea; Obermair, Franz-Josef; Ampenberger, Franziska; Bodenmiller, Bernd; Kopf, Manfred (2020). High-Dimensional T Helper Cell Profiling Reveals a Broad Diversity of Stably Committed Effector States and Uncovers Interlineage Relationships. Immunity, 53(3):597-613.e6. Eling, Nils; Damond, Nicolas; Hoch, Tobias; Bodenmiller, Bernd (2020). Cytomapper: an R/bioconductor package for visualisation of highly multiplexed imaging data. bioRxiv 287516, University of Zurich. Zanotelli, Vito R T; Leutenegger, Matthias; Lun, Xiao-Kang; Georgi, Fanny; de Souza, Natalie; Bodenmiller, Bernd (2020). A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids. bioRxiv 219659, University of Zurich. Lun, Xiao-Kang; Bodenmiller, Bernd (2020). Profiling Cell Signaling Networks at Single-cell Resolution. Molecular & Cellular Proteomics, 19(5):744-756. Chen, William S; Zivanovic, Nevena; van Dijk, David; Wolf, Guy; Bodenmiller, Bernd; Krishnaswamy, Smita (2020). Uncovering axes of variation among single-cell cancer specimens. Nature Methods, 17(3):302-310. Kumar, Sunil; Lun, Xiao-Kang; Bodenmiller, Bernd; Rodríguez Martínez, María; Koeppl, Heinz (2020). Stabilized Reconstruction of Signaling Networks from Single-Cell Cue-Response Data. Scientific Reports, 10:1233. Tognetti, Marco; Gabor, Attila; Yang, Mi; Cappelletti, Valentina; Windhager, Jonas; Charmpi, Konstantina; de Souza, Natalie; Beyer, Andreas; Picotti, Paola; Saez-Rodriguez, Julio; Bodenmiller, Bernd (2020). Deciphering the Signaling Network Landscape of Breast Cancer Improves Drug Sensitivity Prediction. bioRxiv 907691, University of Zurich. Jackson, Hartland W; Fischer, Jana R; Zanotelli, Vito R T; Ali, H Raza; Mechera, Robert; Soysal, Savas D; Moch, Holger; Muenst, Simone; Varga, Zsuzsanna; Weber, Walter P; Bodenmiller, Bernd (2020). The single-cell pathology landscape of breast cancer. Nature, 578(7796):615-620. Crowell, Helena L; Chevrier, Stéphane; Jacobs, Andrea; Sivapatham, Sujana; Bodenmiller, Bernd; Robinson, Mark D; et al; Kölzer, Viktor (2020). An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data. F1000Research, 9:1263. Catena, Raúl; Özcan, Alaz; Kütt, Laura; Plüss, Alex; Schraml, Peter; Moch, Holger; Bodenmiller, Bernd (2020). Highly multiplexed molecular and cellular mapping of breast cancer tissue in three dimensions using mass tomography. bioRxiv 113571, University of Zurich. Wade, James D; Lun, Xiao-Kang; Zivanovic, Nevena; Voit, Eberhard O; Bodenmiller, Bernd (2020). Mechanistic Model of Signaling Dynamics Across an Epithelial Mesenchymal Transition. Frontiers in Physiology, 11:579117. Michael Krauthammer CSV EndNote BibTeX XML Export 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. Wang, Xuefeng; Yu, Xiaoqing; Krauthammer, Michael; Hugo, Willy; Duan, Chunzhe; Kanetsky, Peter A; Teer, Jamie K; Thompson, Zachary J; Kalos, Denise; Tsai, Kenneth Y; Smalley, Keiran SM; Sondak, Vernon K; Chen, Y Ann; Conejo-Garcia, Jose R (2020). The association of MUC16 mutation with tumor mutation burden and its prognostic implications in cutaneous melanoma. Cancer Epidemiology Biomarkers & Prevention, 29(9):1792-1799. Böhlen, Michael Hanspeter; Dolmatova, Oksana; Krauthammer, Michael; Mariyagnanaseelan, Alphonse; Stahl, Jonathan; Surbeck, Timo (2020). Iterations for Propensity Score Matching in MonetDB. In: 24thvEuropean Conference on Advances in Databases and Information Systems, ADBIS 2020, Lyon, 25 August 2020 - 27 August 2020. Springer, 189-203. Biller-Andorno, Nikola; Ferrario, Andrea; Joebges, Susanne; Krones, Tanja; Massini, Federico; Barth, Phyllis; Arampatzis, Georgios; Krauthammer, Michael (2020). AI support for ethical decision-making around resuscitation: proceed with care. medRxiv 20171769, University of Zurich. Frick-Cheng, Arwen E; Sintsova, Anna; Smith, Sara N; Krauthammer, Michael; Eaton, Kathryn A; Mobley, Harry L T (2020). The Gene Expression Profile of Uropathogenic Escherichia coli in Women with Uncomplicated Urinary Tract Infections Is Recapitulated in the Mouse Model. mBio, 11(4):e01412-20.. Vokinger, Kerstin Noëlle; Stekhoven, Daniel J; Krauthammer, Michael (2020). Lost in anonymization — A data anonymization reference classification merging legal and technical considerations. Journal of Law, Medicine & Ethics, 48(1):228-231. Marquart, Kim F; Allam, Ahmed; Janjuha, Sharan; Sintsova, Anna; Villiger, Lukas; Frey, Nina; Krauthammer, Michael; Schwank, Gerald (2020). Predicting base editing outcomes with an attention-based deep learning algorithm trained on high-throughput target library screens. bioRxiv 186544, University of Zurich. Rolf Kümmerli CSV EndNote BibTeX XML Export Figueiredo, Alexandre R T; Kümmerli, Rolf (2020). Microbial Mutualism: Will You Still Need Me, Will You Still Feed Me?. Current Biology, 30(18):R1041-R1043. Rezzoagli, Chiara; Archetti, Martina; Mignot, Ingrid; Baumgartner, Michael; Kümmerli, Rolf (2020). Combining antibiotics with antivirulence compounds can have synergistic effects and reverse selection for antibiotic resistance in Pseudomonas aeruginosa. PLoS Biology, 18(8):e3000805. Gu, Shaohua; Wei, Zhong; Shao, Zhengying; Friman, Ville-Petri; Cao, Kehao; Yang, Tianjie; Kramer, Jos; Wang, Xiaofang; Li, Mei; Mei, Xinlan; Xu, Yangchun; Shen, Qirong; Kümmerli, Rolf; Jousset, Alexandre (2020). Competition for iron drives phytopathogen control by natural rhizosphere microbiomes. Nature Microbiology, 5(8):1002-1010. Niggli, Selina; Kümmerli, Rolf (2020). Strain Background, Species Frequency, and Environmental Conditions Are Important in Determining Pseudomonas aeruginosa and Staphylococcus aureus Population Dynamics and Species Coexistence. Applied and Environmental Microbiology, 86(18):e00962-20. Sathe, Santosh; Kümmerli, Rolf (2020). Antagonistic interactions subdue inter‐species green‐beard cooperation in bacteria. Journal of Evolutionary Biology, 33:1245-1255. Kramer, Jos; Özkaya, Özhan; Kümmerli, Rolf (2020). Bacterial siderophores in community and host interactions. Nature Reviews. Microbiology, 18(3):152-163. Rezzoagli, Chiara; Granato, Elisa T; Kümmerli, Rolf (2020). Harnessing bacterial interactions to manage infections: a review on the opportunistic pathogen Pseudomonas aeruginosa as a case example. Journal of Medical Microbiology, 69(2):147-161. Kramer, Jos; López Carrasco, Miguel Ángel; Kümmerli, Rolf (2020). Positive linkage between bacterial social traits reveals that homogeneous rather than specialised behavioral repertoires prevail in natural Pseudomonas communities. FEMS Microbiology Ecology, 96(1):fiz185. Bjoern Menze CSV EndNote BibTeX XML Export 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. Herhaus, Peter; Lipkova, Jana; Lammer, Felicitas; Yakushev, Igor; Vag, Tibor; Slotta-Huspenina, Julia; Habringer, Stefan; Lapa, Constantin; Pukrop, Tobias; Hellwig, Dirk; Wiestler, Benedikt; Buck, Andreas K; Deckert, Martina; Wester, Hans-Jürgen; Bassermann, Florian; Schwaiger, Markus; Weber, Wolfgang; Menze, Björn; Keller, Ulrich (2020). CXCR4-Targeted PET Imaging of Central Nervous System B-Cell Lymphoma. Journal of Nuclear Medicine, 61(12):1765-1771. Gómez, Pedro A; Cencini, Matteo; Golbabaee, Mohammad; Schulte, Rolf F; Pirkl, Carolin; Horvath, Izabela; Fallo, Giada; Peretti, Luca; Tosetti, Michela; Menze, Bjoern H; Buonincontri, Guido (2020). Rapid three-dimensional multiparametric MRI with quantitative transient-state imaging. Scientific Reports, 10:13769. Schoppe, Oliver; Pan, Chenchen; Coronel, Javier; Mai, Hongcheng; Rong, Zhouyi; Todorov, Mihail Ivilinov; Müskes, Annemarie; Navarro, Fernando; Li, Hongwei; Ertürk, Ali; Menze, Bjoern H (2020). Deep learning-enabled multi-organ segmentation in whole-body mouse scans. Nature Communications, 11:5626. Liu, Xin; Gómez, Pedro A; Solana, Ana Beatriz; Wiesinger, Florian; Menzel, Marion I; Menze, Bjoern H (2020). Silent 3D MR sequence for quantitative and multicontrast T1 and proton density imaging. Physics in Medicine and Biology, 65(18):185010. 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 (2020). Spatial Distribution of Focal Lesions in Whole-Body MRI and Influence of MRI Protocol on Staging in Patients with Smoldering Multiple Myeloma According to the New SLiM-CRAB-Criteria. Cancers, 12(9):2537. Magdalini Polymenidou CSV EndNote BibTeX XML Export Hutten, Saskia; Usluer, Sinem; Bourgeois, Benjamin; Simonetti, Francesca; Odeh, Hana M; Fare, Charlotte M; Czuppa, Mareike; Hruska-Plochan, Marian; Hofweber, Mario; Polymenidou, Magdalini; Shorter, James; Edbauer, Dieter; Madl, Tobias; Dormann, Dorothee (2020). Nuclear import receptors directly bind to arginine-rich dipeptide repeat proteins and suppress their pathological interactions. Cell Reports, 33(12):108538. Zbinden, Aurélie; Pérez-Berlanga, Manuela; De Rossi, Pierre; Polymenidou, Magdalini (2020). Phase separation and neurodegenerative diseases: a disturbance in the force. Developmental Cell, 55(1):45-68. Polymenidou, Magdalini (2020). A Gut Feeling about C9ORF72. Trends in Immunology, 41(9):755-757. Scekic-Zahirovic, Jelena; Sanjuan-Ruiz, Inmaculada; Kan, Vanessa; Megat, Salim; De Rossi, Pierre; Dieterlé, Stéphane; Cassel, Raphaelle; Kessler, Pascal; Wiesner, Diana; Tzeplaeff, Laura; Demais, Valérie; Muller, Hans-Peter; Picchiarelli, Gina; Mishra, Nibha; Dirrig-Grosch, Sylvie; Kassubek, Jan; Rasche, Volker; Ludolph, Albert; Boutillier, Anne-Laurence; Polymenidou, Magdalini; Lagier-Tourenne, Clotilde; Liebscher, Sabine; Dupuis, Luc (2020). Cytoplasmic accumulation of FUS triggers early behavioral alterations linked to cortical neuronal hyperactivity and defects in inhibitory synapses. arXiv.org 141556, University of Zurich. Sahadevan, Sonu; Hembach, Katharina M; Tantardini, Elena; Pérez-Berlanga, Manuela; Hruska-Plochan, Marian; Weber, Julien; Schwarz, Petra; Dupuis, Luc; Robinson, Mark D; De Rossi, Pierre; Polymenidou, Magdalini (2020). Synaptic accumulation of FUS triggers age-dependent misregulation of inhibitory synapses in ALS-FUS mice. arXiv.org 136010, University of Zurich. 2019 Bernd Bodenmiller CSV EndNote BibTeX XML Export Klufa, Jörg; Bauer, Thomas; Hanson, Buck; Herbold, Craig; Starkl, Philipp; Lichtenberger, Beate; Srutkova, Dagmar; Schulz, Daniel; Vujic, Igor; Mohr, Thomas; Rappersberger, Klemens; Bodenmiller, Bernd; Kozakova, Hana; Knapp, Sylvia; Loy, Alexander; Sibilia, Maria (2019). Hair eruption initiates and commensal skin microbiota aggravate adverse events of anti-EGFR therapy. Science Translational Medicine, 11(522):eaax2693. Schulz, Daniel; Severin, Yannik; Zanotelli, Vito Riccardo Tomaso; Bodenmiller, Bernd (2019). In-Depth Characterization of Monocyte-Derived Macrophages using a Mass Cytometry-Based Phagocytosis Assay. Scientific Reports, 9:1925. Arnol, Damien; Schapiro, Denis; Bodenmiller, Bernd; Saez-Rodriguez, Julio; Stegle, Oliver (2019). Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis. Cell Reports, 29(1):202-211.e6. Corrò, Claudia; Healy, Marc E; Engler, Stefanie; Bodenmiller, Bernd; Li, Zhe; Schraml, Peter; Weber, Achim; Frew, Ian J; Rechsteiner, Markus; Moch, Holger (2019). IL-8 and CXCR1 expression is associated with cancer stem cell-like properties of clear cell renal cancer. Journal of Pathology, 248(3):377-389. Lun, Xiao-Kang; Szklarczyk, Damian; Gábor, Attila; Dobberstein, Nadine; Zanotelli, Vito Riccardo Tomaso; Saez-Rodriguez, Julio; von Mering, Christian; Bodenmiller, Bernd (2019). Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling. Molecular Cell, 74(5):1086-1102.e5. Wagner, Johanna; Rapsomaniki, Maria Anna; Chevrier, Stéphane; Anzeneder, Tobias; Langwieder, Claus; Dykgers, August; Rees, Martin; Ramaswamy, Annette; Muenst, Simone; Soysal, Savas Deniz; Jacobs, Andrea; Windhager, Jonas; Silina, Karina; van den Broek, Maries; Dedes, Konstantin Johannes; Rodríguez Martínez, Maria; Weber, Walter Paul; Bodenmiller, Bernd (2019). A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer. Cell, 177(5):1330-1345. Damond, Nicolas; Engler, Stefanie; Zanotelli, Vito R T; Schapiro, Denis; Wasserfall, Clive H; Kusmartseva, Irina; Nick, Harry S; Thorel, Fabrizio; Herrera, Pedro L; Atkinson, Mark A; Bodenmiller, Bernd (2019). A Map of Human Type 1 Diabetes Progression by Imaging Mass Cytometry. Cell Metabolism, 29(3):755-768.e5. Michael Krauthammer CSV EndNote BibTeX XML Export Allam, Ahmed; Nagy, Mate; Thoma, George; Krauthammer, Michael (2019). Neural networks versus Logistic regression for 30 days all-cause readmission prediction. Scientific Reports, 9(1):9277. Krauthammer, Michael. Mobile Health – Eine Technologie wird erwachsen. In: readme : Das Bulletin derUZH Alumni Informatik, 41, 1 September 2019, p.3-5. Halaban, Ruth; Bacchiocchi, Antonella; Straub, Robert; Cao, Jian; Sznol, Mario; Narayan, Deepak; Allam, Ahmed; Krauthammer, Michael; Mansour, Tarek S (2019). A novel anti-melanoma SRC-family kinase inhibitor. OncoTarget, 10(23):2237-2251. Rolf Kümmerli CSV EndNote BibTeX XML Export Sathe, Santosh; Mathew, Anugraha; Agnoli, Kirsty; Eberl, Leo; Kümmerli, Rolf (2019). Genetic architecture constrains exploitation of siderophore cooperation in the bacterium Burkholderia cenocepacia. Evolution Letters, 3(6):610-622. O'Brien, Siobhán; Kümmerli, Rolf; Paterson, Steve; Winstanley, Craig; Brockhurst, Michael A (2019). Transposable temperate phages promote the evolution of divergent social strategies in Pseudomonas aeruginosa populations. Proceedings of the Royal Society of London, Series B: Biological Sciences, 286(1912):20191794. Rezzoagli, Chiara; Granato, Elisa T; Kümmerli, Rolf (2019). In-vivo microscopy reveals the impact of Pseudomonas aeruginosa social interactions on host colonization. The ISME journal, 13(10):2403-2414. Wechsler, Tobias; Kümmerli, Rolf; Dobay, Akos (2019). Understanding policing as a mechanism of cheater control in cooperating bacteria. Journal of Evolutionary Biology, 32(5):412-424. Schiessl, Konstanze T; Ross‐Gillespie, Adin; Cornforth, Daniel M; Weigert, Michael; Bigosch, Colette; Brown, Sam P; Ackermann, Martin; Kümmerli, Rolf (2019). Individual‐ versus group‐optimality in the production of secreted bacterial compounds. Evolution, 73(4):675-688. Magdalini Polymenidou CSV EndNote BibTeX XML Export Afroz, Tariq; Pérez-Berlanga, Manuela; Polymenidou, Magdalini (2019). Structural Transition, Function and Dysfunction of TDP-43 in Neurodegenerative Diseases. CHIMIA International Journal for Chemistry, 73(5):380-390. Jawaid, Ali; Woldemichael, Bisrat T; Kremer, Eloïse A; Laferriere, Florent; Gaur, Niharika; Afroz, Tariq; Polymenidou, Magdalini; Mansuy, Isabelle M (2019). Memory decline and its reversal in aging and neurodegeneration involve miR-183/96/182 biogenesis. Molecular Neurobiology, 56(5):3451-3462. Loughlin, Fionna E; Lukavsky, Peter J; Kazeeva, Tamara; Reber, Stefan; Hock, Eva-Maria; Colombo, Martino; Von Schroetter, Christine; Pauli, Phillip; Cléry, Antoine; Mühlemann, Oliver; Polymenidou, Magdalini; Ruepp, Marc-David; Allain, Frédéric H-T (2019). The Solution Structure of FUS Bound to RNA Reveals a Bipartite Mode of RNA Recognition with Both Sequence and Shape Specificity. Molecular Cell, 73(3):490-504.e6. Laferrière, Florent; Maniecka, Zuzanna; Pérez-Berlanga, Manuela; Hruska-Plochan, Marian; Gilhespy, Larissa; Hock, Eva-Maria; Wagner, Ulrich; Afroz, Tariq; Boersema, Paul J; Barmettler, Gery; Foti, Sandrine C; Asi, Yasmine T; Isaacs, Adrian M; Al-Amoudi, Ashraf; Lewis, Amanda; Stahlberg, Henning; Ravits, John; De Giorgi, Francesca; Ichas, François; Bezard, Erwan; Picotti, Paola; Lashley, Tammaryn; Polymenidou, Magdalini (2019). TDP-43 extracted from frontotemporal lobar degeneration subject brains displays distinct aggregate assemblies and neurotoxic effects reflecting disease progression rates. Nature Neuroscience, 22(1):65-77.