DQBM Publications

ZORA Publication List

Publications

• 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, Cold Spring Harbor Laboratory.
• 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, Cold Spring Harbor Laboratory.
• 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.

ZORA Publication List

Publications

• 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, Cold Spring Harbor Laboratory.
• 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.

ZORA Publication List

Publications

• 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, Cold Spring Harbor Laboratory.
• 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, Cornell University.
• 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.org 2204.11351, Cornell University.
• 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; 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.
• 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 Juni 2022 - 17 Juni 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 Juni 2022 - 17 Juni 2022, NTCIR.

ZORA Publication List

Publications

• 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 Pseudomonas aeruginosa Can Occur via Loss of Function and Regulon Modulation. mSystems, 7(5):e0035422.
• 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, 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.
• 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.

ZORA Publication List

Publications

• 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 Pattern Analysis and Machine Intelligence, 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, Cornell University.
• Wittmann, Bastian; Navarro, Fernando; Shit, Suprosanna; Menze, Bjoern H (2022). Focused Decoding Enables 3D Anatomical Detection by Transformers. ArXiv.org 2207.10774, Cornell University.
• 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, Cornell University.
• 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, Cornell University.
• 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, Cornell University.
• 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.
• 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 22276371, Cold Spring Harbor Laboratory.
• 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.
• 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, 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.
• 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, Cornell University.
• 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, Cornell University.
• 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.

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Publications

• 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. The EMBO Journal, 41(23):e112338.
• Wiersma, Vera I; Rigort, Ruben; Polymenidou, Magdalini (2022). Tau: a phase in the crowd. The EMBO Journal, 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, Cold Spring Harbor Laboratory.
• 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, 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.

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Publications

• Windhager, Jonas; Bodenmiller, Bernd; Eling, Nils (2021). An end-to-end workflow for multiplexed image processing and analysis. bioRxiv 468357, Cold Spring Harbor Laboratory.
• 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, Cold Spring Harbor Laboratory.
• 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.
• 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, 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.

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Publications

• 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.

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Publications

• 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.

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Publications

• 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, Cold Spring Harbor Laboratory.
• 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, Cold Spring Harbor Laboratory.

ZORA Publication List

Publications

• 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, Cornell University.
• 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, Cold Spring Harbor Laboratory.
• 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, Cornell University.
• 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, Cornell University.
• 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, Cornell University.
• 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, Cornell University.
• 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.

Pagination

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• 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.

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• 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, Cold Spring Harbor Laboratory.
• 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, Cold Spring Harbor Laboratory.
• 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, Cold Spring Harbor Laboratory.
• 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, Cold Spring Harbor Laboratory.
• 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, Cold Spring Harbor Laboratory.
• 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.

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• 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, Cold Spring Harbor Laboratory.
• 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, Cold Spring Harbor Laboratory.

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• 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.

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Publications

• 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.

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Publications

• 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, Cornell University.
• 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, Cornell University.

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• 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 R T; 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 R T; 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.

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Publications

• 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, 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.

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Publications

• 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.

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Publications

• 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.