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2024

Amiranashvili, Tamaz; Lüdke, David; Li, Hongwei Bran; Zachow, Stefan; Menze, Bjoern H (2024). Learning continuous shape priors from sparse data with neural implicit functions. Medical Image Analysis, 94:103099.

Ruchti, Fiorella. Immunity to the Skin Commensal Yeast $\textit{Malassezia}$ in Healthy and Atopic Skin. 2024, University of Zurich, Faculty of Science.

Cords, Lena; Engler, Stefanie; Haberecker, Martina; Rüschoff, Jan Hendrik; Moch, Holger; de Souza, Natalie; Bodenmiller, Bernd (2024). Cancer-associated fibroblast phenotypes are associated with patient outcome in non-small cell lung cancer. Cancer Cell, 42(3):396-412.e5.

de Souza, Natalie; Zhao, Shan; Bodenmiller, Bernd (2024). Multiplex protein imaging in tumour biology. Nature Reviews Cancer, 24(3):171-191.

Fontana, Elena; Bongianni, Matilde; Benussi, Alberto; Bronzato, Erika; Scialo, Carlo; Sacchetto, Luca; Cagnin, Annachiara; Castriciano, Santina; Buratti, Emanuele; Gardoni, Fabrizio; Italia, Maria; Schreiber, Alberto; Ferracin, Chiara; Fiorini, Michele; Newell, Kathy L.; Cracco, Laura; Garringer, Holly J.; Cecchini, Maria Paola; Polymenidou, Magdalini; Padovani, Alessandro; Monaco, Salvatore; Legname, Giuseppe; Ghetti, Bernardino; Borroni, Barbara; Zanusso, Gianluigi (2024). Detection of TDP-43 seeding activity in the olfactory mucosa from patients with frontotemporal dementia. Alzheimer's & Dementia, 20(2):1156-1165.

Wang, Nanqi; Wang, Tianqi; Chen, Yu; Wang, Ming; Lu, Qiaofang; Wang, Kunguang; Dou, Zhechao; Chi, Zhiguang; Qiu, Wei; Dai, Jing; Niu, Lei; Cui, Jianyu; Wei, Zhong; Zhang, Fusuo; Kümmerli, Rolf; Zuo, Yuanmei (2024). Microbiome convergence enables siderophore-secreting-rhizobacteria to improve iron nutrition and yield of peanut intercropped with maize. Nature Communications, 15(1):839.

Meyer, Lasse; Eling, Nils; Bodenmiller, Bernd (2024). cytoviewer: an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data. BMC Bioinformatics, 25(1):9.

Balázs, Zsolt; Gitchev, Todor; Ivanković, Ivna; Krauthammer, Michael (2024). Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis. Bioinformatics, 40(1):btae017.

Sudre, Carole H; Van Wijnen, Kimberlin; Dubost, Florian; Adams, Hieab; Atkinson, David; Barkhof, Frederik; Birhanu, Mahlet A; Bron, Esther E; Camarasa, Robin; Chaturvedi, Nish; Chen, Yuan; Chen, Zihao; Chen, Shuai; Dou, Qi; Evans, Tavia; Ezhov, Ivan; Gao, Haojun; Girones Sanguesa, Marta; Gispert, Juan Domingo; Gomez Anson, Beatriz; Hughes, Alun D; Ikram, M Arfan; Ingala, Silvia; Jaeger, H Rolf; Kofler, Florian; Kuijf, Hugo J; Kutnar, Denis; Lee, Minho; Li, Bo; Lorenzini, Luigi; et al (2024). Where is VALDO? VAscular Lesions Detection and segmentatiOn challenge at MICCAI 2021. Medical Image Analysis, 91:103029.

Vollenweider, Vera; Rehm, Karoline; Chepkirui, Clara; Pérez-Berlanga, Manuela; Polymenidou, Magdalini; Piel, Jörn; Bigler, Laurent; Kümmerli, Rolf (2024). Antimicrobial activity of iron-depriving pyoverdines against human opportunistic pathogens. eLife, 13:RP92493.

Prabhakar, Chinmay; Shit, Suprosanna; Paetzold, Johannes C; Ezhov, Ivan; Koner, Rajat; Li, Hongwei; Kofler, Florian Sebastian; Menze, Bjoern (2024). Vesselformer: Towards Complete 3D Vessel Graph Generation from Images. In: Medical Imaging with Deep Learning, Nashville, Tennessee, 10 July 2023 - 12 July 2023. MLResearch Press, 320-331.

Prabhakar, Chinmay; Li, Hongwei; Yang, Jiancheng; Shit, Suprosanna; Wiestler, Benedikt; Menze, Bjoern (2024). ViT-AE++: Improving Vision Transformer Autoencoder for Self-supervised Medical Image Representations. In: Medical Imaging with Deep Learning, Nashville, 10 July 2023 - 12 July 2023. MLResearch Press, 666-679.

2023

Vladimirov, Nikita; Voigt, Fabian F; Naert, Thomas; Araujo, Gabriela R; Cai, Ruiyao; Reuss, Anna Maria; Zhao, Shan; Schmid, Patricia; Hildebrand, Sven; Schaettin, Martina; Groos, Dominik; Mateos, José María; Bethge, Philipp; Yamamoto, Taiyo; Aerne, Valentino; Roebroeck, Alard; Ertürk, Ali; Aguzzi, Adriano; Ziegler, Urs; Stoeckli, Esther; Baudis, Laura; Lienkamp, Soeren S; Helmchen, Fritjof (2023). The Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for large cleared samples. bioRxiv 2023.06.16, University of Zurich.

Graf, Robert; Schmitt, Joachim; Schlaeger, Sarah; Möller, Hendrik Kristian; Sideri-Lampretsa, Vasiliki; Sekuboyina, Anjany; Krieg, Sandro Manuel; Wiestler, Benedikt; Menze, Bjoern; Rueckert, Daniel; Kirschke, Jan Stefan (2023). Denoising diffusion-based MRI to CT image translation enables automated spinal segmentation. European Radiology Experimental, 7(1):70.

Windhager, Jonas; Zanotelli, Vito R T; Schulz, Daniel; Meyer, Lasse; Daniel, Michelle; Bodenmiller, Bernd; Eling, Nils (2023). An end-to-end workflow for multiplexed image processing and analysis. Nature Protocols, 18(11):3565-3613.

Kaushik, Sandeep S; Bylund, Mikael; Cozzini, Cristina; Shanbhag, Dattesh; Petit, Steven F; Wyatt, Jonathan J; Menzel, Marion I; Pirkl, Carolin; Mehta, Bhairav; Chauhan, Vikas; Chandrasekharan, Kesavadas; Jonsson, Joakim; Nyholm, Tufve; Wiesinger, Florian; Menze, Bjoern (2023). Region of interest focused MRI to synthetic CT translation using regression and segmentation multi-task network. Physics in Medicine and Biology, 68(19):195003.

Buchner, Josef A; Peeken, Jan C; Etzel, Lucas; Ezhov, Ivan; Mayinger, Michael; Christ, Sebastian M; Brunner, Thomas B; Wittig, Andrea; Menze, Bjoern H; Zimmer, Claus; Meyer, Bernhard; Guckenberger, Matthias; Andratschke, Nicolaus; El Shafie, Rami A; Debus, Jürgen; Rogers, Susanne; Riesterer, Oliver; Schulze, Katrin; Feldmann, Horst J; Blanck, Oliver; Zamboglou, Constantinos; Ferentinos, Konstantinos; Bilger, Angelika; Grosu, Anca L; Wolff, Robert; Kirschke, Jan S; Eitz, Kerstin A; Combs, Stephanie E; Bernhardt, Denise; Rueckert, Daniel; et al (2023). Identifying core MRI sequences for reliable automatic brain metastasis segmentation. Radiotherapy and Oncology, 188:109901.

Pérez-Berlanga, Manuela; Wiersma, Vera I; Zbinden, Aurélie; De Vos, Laura; Wagner, Ulrich; Foglieni, Chiara; Mallona, 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 (2023). Loss of TDP-43 oligomerization or RNA binding elicits distinct aggregation patterns. EMBO Journal Online, 42(17):e111719.

Hosogane, Tsuyoshi; Casanova, Ruben; Bodenmiller, Bernd (2023). DNA-barcoded signal amplification for imaging mass cytometry enables sensitive and highly multiplexed tissue imaging. Nature Methods, 20(9):1304-1309.

Strotton, Merrick; Hosogane, Tsuyoshi; di Michiel, Marco; Moch, Holger; Varga, Zsuzsanna; Bodenmiller, Bernd (2023). Multielement Z-tag imaging by X-ray fluorescence microscopy for next-generation multiplex imaging. Nature Methods, 20(9):1310-1322.

Shaitarova, Anastassia; Zaghir, Jamil; Lavelli, Alberto; Krauthammer, Michael; Rinaldi, Fabio (2023). Exploring the Latest Highlights in Medical Natural Language Processing across Multiple Languages: A Survey. Yearbook of medical informatics, 32(01):230-243.

Kümmerli, Rolf (2023). Iron acquisition strategies in pseudomonads: mechanisms, ecology, and evolution. Biometals, 36(4):777-797.

Mathis, Nicolas; Allam, Ahmed; Kissling, Lucas; Marquart, Kim Fabiano; Schmidheini, Lukas; Solari, Cristina; Balázs, Zsolt; Krauthammer, Michael; Schwank, Gerald (2023). Predicting prime editing efficiency and product purity by deep learning. Nature Biotechnology, 41(8):1151-1159.

Payette, Kelly; Li, Hongwei Bran; de Dumast, Priscille; Licandro, Roxane; Ji, Hui; Siddiquee, Md Mahfuzur Rahman; Xu, Daguang; Myronenko, Andriy; Liu, Hao; Pei, Yuchen; Wang, Lisheng; Peng, Ying; Xie, Juanying; Zhang, Huiquan; Dong, Guiming; Fu, Hao; Wang, Guotai; Rieu, ZunHyan; Kim, Donghyeon; Kim, Hyun Gi; Karimi, Davood; Gholipour, Ali; Torres, Helena R; Oliveira, Bruno; Vilaça, João L; Lin, Yang; Avisdris, Netanell; Ben-Zvi, Ori; Bashat, Dafna Ben; Fidon, Lucas; Menze, Bjoern; Jakab, András; et al (2023). Fetal brain tissue annotation and segmentation challenge results. Medical Image Analysis, 88:102833.

Yassini, Nima; Sprenger, Janine; Pastor Arroyo, Eva Maria; Krudewig, Christiane; Pellegrini, Giovanni; Joller, Nicole; Wagner, Carsten A; Imenez Silva, Pedro Henrique (2023). Ovarian cancer G protein-coupled receptor 1 deficiency exacerbates crystal deposition and kidney injury in oxalate nephropathy in female mice. Clinical Science, 137(14):1013-1025.

Schmitz, Désirée A; Allen, Richard C; Kümmerli, Rolf (2023). Negative interactions and virulence differences drive the dynamics in multispecies bacterial infections. Proceedings of the Royal Society of London, Series B: Biological Sciences, 290(2003):20231119.

Cords, Lena; Tietscher, Sandra; Anzeneder, Tobias; Langwieder, Claus; Rees, Martin; de Souza, Natalie; Bodenmiller, Bernd (2023). Cancer-associated fibroblast classification in single-cell and spatial proteomics data. Nature Communications, 14(1):4294.

Garaiman, Alexandru; Nooralahzadeh, Farhad; Mihai, Carina; Gonzalez, Nicolas Perez; Gkikopoulos, Nikitas; Becker, Mike Oliver; Distler, Oliver; Krauthammer, Michael; Maurer, Britta (2023). Vision transformer assisting rheumatologists in screening for capillaroscopy changes in systemic sclerosis: an artificial intelligence model. Rheumatology, 62(7):2492-2500.

Zhao, Yu; Tang, Chunmeng; Cui, Bihao; Somasundaram, Arun; Raspe, Johannes; Hu, Xiaobin; Holzapfel, Christina; Junker, Daniela; Hauner, Hans; Menze, Bjoern; Wu, Mingming; Karampinos, Dimitrios (2023). Automated segmentation of the human supraclavicular fat depot via deep neural network in water-fat separated magnetic resonance images. Quantitative Imaging in Medicine and Surgery, 13(7):4699-4715.

Kümmerli, Rolf; Frank, Steven A (2023). Evolutionary explanations for heterogeneous behavior in clonal bacterial populations. Trends in Microbiology, 31(7):665-667.

Niggli, Selina; Schwyter, Lukas; Poveda, Lucy; Grossmann, Jonas; Kümmerli, Rolf (2023). Rapid and strain-specific resistance evolution of $Staphylococcus aureu$s against inhibitory molecules secreted by $Pseudomonas aeruginosa$. mBio, 14(5):e0315322.

Trottet, Cécile Claire; Allam, Ahmed; Horvath, Aron N; Micheroli, Raphael; Krauthammer, Michael; Ospelt, Caroline (2023). Explainable Deep Learning for Disease Activity Prediction in Chronic Inflammatory Joint Diseases. In: ICML 3rd Workshop on Interpretable Machine Learning in Healthcare (IMLH), Honolulu, Hawaii, 28 July 2023, 1-8.

Eichhoff, Ossia M; Stoffel, Corinne I; Käsler, Jan; Briker, Luzia; Turko, Patrick; Karsai, Gergely; Zila, Nina; Paulitschke, Verena; Cheng, Phil F; Leitner, Alexander; Bileck, Andrea; Zamboni, Nicola; Irmisch, Anja; Balazs, 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, Reinhard; Levesque, Mitchell Paul (2023). ROS Induction Targets Persister Cancer Cells with Low Metabolic Activity in NRAS-Mutated Melanoma. Cancer Research, 83(7):1128-1146.

de la Rosa, Ezequiel; Sima, Diana M; Kirschke, Jan S; Menze, Bjoern; Robben, David (2023). Detecting CTP truncation artifacts in acute stroke imaging from the arterial input and the vascular output functions. PLoS ONE, 18(3):e0283610.

Fischer, Jana Raja; Jackson, Hartland Warren; de Souza, Natalie; Varga, Zsuzsanna; Schraml, Peter; Moch, Holger; Bodenmiller, Bernd (2023). Multiplex imaging of breast cancer lymph node metastases identifies prognostic single-cell populations independent of clinical classifiers. Cell Reports Medicine, 4(3):100977.

Bost, Pierre; Schulz, Daniel; Engler, Stefanie; Wasserfall, Clive; Bodenmiller, Bernd (2023). Optimizing multiplexed imaging experimental design through tissue spatial segregation estimation. Nature Methods, 20(3):418-423.

Wittmann, Bastian; Navarro, Fernando; Shit, Suprosanna; Menze, Bjoern (2023). Focused Decoding Enables 3D Anatomical Detection by Transformers. Journal of Machine Learning for Biomedical Imaging, 2(February 2):72-95.

Tetteh, Giles; Navarro, Fernando; Meier, Raphael; Kaesmacher, Johannes; Paetzold, Johannes C; Kirschke, Jan S; Zimmer, Claus; Wiest, Roland; Menze, Bjoern H (2023). A deep learning approach to predict collateral flow in stroke patients using radiomic features from perfusion images. Frontiers in Neurology, 14:1039693.

Cordts, Isabell; Wachinger, Annika; Scialo, Carlo; Lingor, Paul; Polymenidou, Magdalini; Buratti, Emanuele; Feneberg, Emily (2023). TDP-43 Proteinopathy Specific Biomarker Development. Amyotrophic Lateral Sclerosis, 12(4):597.

Tchouakui, Magellan; Assatse, Tatiane; Tazokong, Hervé R; Oruni, Ambrose; Menze, Benjamin D; Nguiffo-Nguete, Daniel; Mugenzi, Leon M J; Kayondo, Jonathan; Watsenga, Francis; Mzilahowa, Themba; Osae, Michael; Wondji, Charles S (2023). Detection of a reduced susceptibility to chlorfenapyr in the malaria vector Anopheles gambiae contrasts with full susceptibility in Anopheles funestus across Africa. Scientific Reports, 13(1):2363.

Bilic, Patrick; Christ, Patrick; Li, Hongwei Bran; Vorontsov, Eugene; Ben-Cohen, Avi; Kaissis, Georgios; Szeskin, Adi; Jacobs, Colin; Mamani, Gabriel Efrain Humpire; Chartrand, Gabriel; Lohöfer, Fabian; Holch, Julian Walter; Sommer, Wieland; Hofmann, Felix; Hostettler, Alexandre; Lev-Cohain, Naama; Drozdzal, Michal; Amitai, Michal Marianne; Vivanti, Refael; Sosna, Jacob; Ezhov, Ivan; Sekuboyina, Anjany; Navarro, Fernando; Kofler, Florian; Paetzold, Johannes C; Shit, Suprosanna; Hu, Xiaobin; Lipková, Jana; Rempfler, Markus; Piraud, Marie; et al (2023). The Liver Tumor Segmentation Benchmark (LiTS). Medical Image Analysis, 84:102680.

Stirm, Kristin; Leary, Peter; Wüst, Daria; Stark, Dominique; Joller, Nicole; Karakus, Ufuk; Boyman, Onur; Tzankov, Alexandar; Müller, Anne (2023). Treg-selective IL-2 starvation synergizes with CD40 activation to sustain durable responses in lymphoma models. Journal for ImmunoTherapy of Cancer, 11(2):e006263.

Pati, Sarthak; Baid, Ujjwal; Edwards, Brandon; Sheller, Micah; Wang, Shih-Han; Reina, G Anthony; Foley, Patrick; Gruzdev, Alexey; Karkada, Deepthi; Davatzikos, Christos; Sako, Chiharu; Ghodasara, Satyam; Bilello, Michel; Mohan, Suyash; Vollmuth, Philipp; Brugnara, Gianluca; Preetha, Chandrakanth J; Sahm, Felix; Maier-Hein, Klaus; Zenk, Maximilian; Bendszus, Martin; Wick, Wolfgang; Calabrese, Evan; Rudie, Jeffrey; Villanueva-Meyer, Javier; Cha, Soonmee; Ingalhalikar, Madhura; Jadhav, Manali; Pandey, Umang; Saini, Jitender; et al (2023). Author Correction: Federated learning enables big data for rare cancer boundary detection. Nature Communications, 14(1):436.

Tietscher, Sandra; Wagner, Johanna; Anzeneder, Tobias; Langwieder, Claus; Rees, Martin; Sobottka, Bettina; de Souza, Natalie; Bodenmiller, Bernd (2023). A comprehensive single-cell map of T cell exhaustion-associated immune environments in human breast cancer. Nature Communications, 14(1):98.

Ezhov, Ivan; Scibilia, Kevin; Franitza, Katharina; Steinbauer, Felix; Shit, Suprosanna; Zimmer, Lucas; Lipkova, Jana; Kofler, Florian; Paetzold, Johannes C; Canalini, Luca; Waldmannstetter, Diana; Menten, Martin J; Metz, Marie; Wiestler, Benedikt; Menze, Bjoern (2023). Learn-Morph-Infer: A new way of solving the inverse problem for brain tumor modeling. Medical Image Analysis, 83:102672.

Schwarz, Kyriakos. Deep Learning in Computational Pharmacology. 2023, University of Zurich, Faculty of Science.

Rohanian, Morteza; Nooralahzadeh, Farhad; Rohanian, Omid; Clifton, David; Krauthammer, Michael (2023). Disfluent Cues for Enhanced Speech Understanding in Large Language Models. In: Empirical Methods in Natural Language Processing (EMNLP), Singapore, 2023, 3676-3684.

2022

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.

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.

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.

Pati, Sarthak; Baid, Ujjwal; Edwards, Brandon; et al; Li, Hongwei; Weiss, Tobias; Weller, Michael (2022). Federated learning enables big data for rare cancer boundary detection. Nature Communications, 13(1):7346.

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.

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.

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.

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.

Funnell, Tyler; Bodenmiller, Bernd (2022). Single-cell genomic variation induced by mutational processes in cancer. Nature, 612(7938):106-115.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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, 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 &amp; Generalizability: A Revisit from Medical Imaging Perspective. In: 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Glasgow, Scotland, United Kingdom, 11 July 2022 - 15 July 2022. Institute of Electrical and Electronics Engineers, 5074-5079.

Fidon, Lucas; et al; Menze, Bjoern (2022). A Dempster-Shafer approach to trustworthy AI with application to fetal brain MRI segmentation. ArXiv.org 2204.02779, Cornell University.

Maier-Hein, Lena; et al; Menze, Bjoern (2022). Metrics reloaded: Pitfalls and recommendations for image analysis validation. ArXiv.org 2206.01653, Cornell University.

Amiranashvili, Tamaz; Lüdke, D; Liu, H B; Menze, Bjoern; Zachow, S (2022). Learning Shape Reconstruction from Sparse Measurements with Neural Implicit Functions. In: MIDL 2022, Zurich Switzerland, 6 July 2022. MLResearch Press, 1-13.

Kenigsbuch, Mor; Bost, Pierre; Halevi, Shahar; Chang, Yuzhou; Chen, Shuo; Ma, Qin; Hajbi, Renana; Schwikowski, Benno; Bodenmiller, Bernd; Fu, Hongjun; Schwartz, Michal; Amit, Ido (2022). A shared disease-associated oligodendrocyte signature among multiple CNS pathologies. Nature Neuroscience, 25(7):876-886.

Sollmann, Nico; Löffler, Maximilian T; El Husseini, Malek; Sekuboyina, Anjany; Dieckmeyer, Michael; Rühling, Sebastian; Zimmer, Claus; Menze, Bjoern; Joseph, Gabby B; Baum, Thomas; Kirschke, Jan S (2022). Automated Opportunistic Osteoporosis Screening in Routine Computed Tomography of the Spine: Comparison With Dedicated Quantitative CT. Journal of Bone and Mineral Research, 37(7):1287-1296.

Soichot, Julien; Guttmann, Nathalie; Rehrauer, Hubert; Joller, Nicole; Tritten, Lucienne (2022). Nematode microRNAs can Individually Regulate Interferon Regulatory Factor 4 and mTOR in Differentiating T Helper 2 Lymphocytes and Modulate Cytokine Production in Macrophages. Frontiers in Molecular Biosciences, 9:909312.

Ivankovic, Ivana; Balázs, Zsolt; Gitchev, Todor; Trejo Banos, Daniel; Moldovan, Norbert; Panagiotis, Balermpas; Willmann, Jonas; Andratschke, N; Moulière, Florent; Krauthammer, Michael (2022). A versatile computational pipeline for the preprocessing of cell-free DNA fragmentation data. Cancer Research 82, University of Zurich.

de la Rosa, Ezequiel; et al; Menze, Bjoern H (2022). Detecting CTP Truncation Artifacts in Acute Stroke Imaging from the Arterial Input and the Vascular Output Functions. medRxiv 22276371, Cold Spring Harbor Laboratory.

Ivankovic, Ivna; Balázs, Zsolt; Gitchev, Todor; Banos, Daniel Trejo; Moldovan, Norbert; Balermpas, Panagiotis; Willmann, Jonas; Andratschke, Nicolaus; Moulière, Florent; Krauthammer, Michael (2022). Abstract 1912: A versatile computational pipeline for the preprocessing of cell-free DNA fragmentation data. Cancer Research, 82(12_Supplem):1912.

Petzsche, Moritz Roman Hernandez; et al; Kofler, Florian; Ezhov, Ivan; Menze, Bjoern (2022). ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset. ArXiv.org 2206.06694, Cornell University.

Al Boustani, George; Weiß, Lennart Jakob Konstantin; Li, Hongwei; Meyer, Svea Marie; Hiendlmeier, Lukas; Rinklin, Philipp; Menze, Bjoern; Hemmert, Werner; Wolfrum, Bernhard (2022). Influence of Auditory Cues on the Neuronal Response to Naturalistic Visual Stimuli in a Virtual Reality Setting. Frontiers in Human Neuroscience, 16:809293.

Dieckmeyer, Michael; Löffler, Maximilian Thomas; El Husseini, Malek; Sekuboyina, Anjany; Menze, Bjoern; Sollmann, Nico; Wostrack, Maria; Zimmer, Claus; Baum, Thomas; Kirschke, Jan Stefan (2022). Level-Specific Volumetric BMD Threshold Values for the Prediction of Incident Vertebral Fractures Using Opportunistic QCT: A Case-Control Study. Frontiers in Endocrinology, 13:882163.

Kofler, Florian; et al; Menze, Bjoern (2022). Deep Quality Estimation: Creating Surrogate Models for Human Quality Ratings. ArXiv.org 2205.10355, Cornell University.

Wiersma, Vera I; Rigort, Ruben; Polymenidou, Magdalini (2022). Tau: a phase in the crowd. EMBO Journal Online, 41:e111425.

Mridha, Subham; Kümmerli, Rolf (2022). Enforced specialization fosters mutual cheating and not division of labour in the bacterium Pseudomonas aeruginosa. Journal of Evolutionary Biology, 35(5):719-730.

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.

Danenberg, Esther; Bardwell, Helen; Zanotelli, Vito R T; Provenzano, Elena; Chin, Suet-Feung; Rueda, Oscar M; Green, Andrew; Rakha, Emad; Aparicio, Samuel; Ellis, Ian O; Bodenmiller, Bernd; Caldas, Carlos; Ali, H Raza (2022). Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature Genetics, 54(5):660-669.

Pastor Arroyo, Eva Maria; Yassini, Nima; Sakiri, Elif; Russo, Giancarlo; Bourgeois, Soline; Mohebbi, Nilufar; Amann, Kerstin; Joller, Nicole; Wagner, Carsten A; Imenez Silva, Pedro Henrique (2022). Alkali therapy protects renal function, suppresses inflammation, and improves cellular metabolism in kidney disease. Clinical Science, 136(8):557-577.

Estrada Brull, Anna; Panetti, Camilla; Joller, Nicole (2022). Moving to the Outskirts: Interplay Between Regulatory T Cells and Peripheral Tissues. Frontiers in Immunology, 13:864628.

Xue, Song; Gafita, Andrei; Dong, Chao; Zhao, Yu; Tetteh, Giles; Menze, Bjoern H; Ziegler, Sibylle; Weber, Wolfgang; Afshar-Oromieh, Ali; Rominger, Axel; Eiber, Matthias; Shi, Kuangyu (2022). Proof-of-concept Study to Estimate Individual Post-Therapy Dosimetry in Men with Advanced Prostate Cancer Treated with 177Lu-PSMA I&T Therapy. Research Square 1588151/v1, University of Zurich.

Yuan, Han; Liu, Minxuan; Kang, Lican; Chenkui, Miao; Wu, Ying; et al; Krauthammer, Michael (2022). An empirical study of the effect of background data size on the stability of SHapley Additive exPlanations (SHAP) for deep learning models. ArXiv.org 2204.11351, Cornell University.

Jayakumar, Priyanikha; Figueiredo, Alexandre R T; Kümmerli, Rolf (2022). Evolution of the quorum sensing systems in Pseudomonas aeruginosa can involve both loss of regulon function and network modulation. bioRxiv 489656, Cold Spring Harbor Laboratory.

Finck, Tom; Li, Hongwei; Schlaeger, Sarah; Grundl, Lioba; Sollmann, Nico; Bender, Benjamin; Bürkle, Eva; Zimmer, Claus; Kirschke, Jan; Menze, Björn; Mühlau, Mark; Wiestler, Benedikt (2022). Uncertainty-Aware and Lesion-Specific Image Synthesis in Multiple Sclerosis Magnetic Resonance Imaging: A Multicentric Validation Study. Frontiers in Neuroscience, 16:889808.

de Vargas Roditi, Laura; Jacobs, Andrea; Rueschoff, Jan H; Bankhead, Pete; Chevrier, Stéphane; Jackson, Hartland Warren; Hermanns, Thomas; Fankhauser, Christian Daniel; Poyet, Cédric; Chun, Felix; Rupp, Niels J; Tschaebunin, Alexandra; Bodenmiller, Bernd; Wild, Peter Johannes (2022). Single-cell proteomics defines the cellular heterogeneity of localized prostate cancer. Cell Reports Medicine, 3(4):100604.

Bieri, Uwe; Scharl, Michael; Sigg, Silvan; Szczerba, Barbara Maria; Morsy, Yasser; Rüschoff, Jan Hendrik; Schraml, Peter Hans; Krauthammer, Michael; Hefermehl, Lukas John; Eberli, Daniel; Poyet, Cédric (2022). Prospective observational study of the role of the microbiome in BCG responsiveness prediction (SILENT-EMPIRE): a study protocol. BMJ Open, 12(4):e061421.

Hiltbrunner, Stefanie; Cords, Lena; Kasser, Sabrina; Freiberger, Sandra N; Kreutzer, Susanne; Toussaint, Nora C; Grob, Linda; Opitz, Isabelle; Messerli, Michael; Zoche, Martin; Soltermann, Alex; Rechsteiner, Markus; van den Broek, Maries; Bodenmiller, Bernd; Curioni-Fontecedro, Alessandra (2022). Acquired resistance to anti-PD1 therapy in patients with NSCLC reveals changes in T cell phenotypes and MET amplification. bioRxiv 487590v1, Cold Spring Harbor Laboratory.

Rühling, Sebastian; Scharr, Andreas; Sollmann, Nico; Wostrack, Maria; Löffler, Maximilian T; Menze, Bjoern; Sekuboyina, Anjany; El Husseini, Malek; Braren, Rickmer; Zimmer, Claus; Kirschke, Jan S (2022). Proposed diagnostic volumetric bone mineral density thresholds for osteoporosis and osteopenia at the cervicothoracic spine in correlation to the lumbar spine. European Radiology, 32(9):6207-6214.

Ivantsits, Matthias; Goubergrits, Leonid; Menze, Bjoern; et al (2022). Detection and analysis of cerebral aneurysms based on X-ray rotational angiography - the CADA 2020 challenge. Medical Image Analysis, 77:102333.

Pirkl, Carolin M; Cencini, Matteo; Kurzawski, Jan W; Waldmannstetter, Diana; Li, Hongwei; Sekuboyina, Anjany; Endt, Sebastian; Peretti, Luca; Donatelli, Graziella; Pasquariello, Rosa; Costagli, Mauro; Buonincontri, Guido; Tosetti, Michela; Menzel, Marion I; Menze, Bjoern H (2022). Learning residual motion correction for fast and robust 3D multiparametric MRI. Medical Image Analysis, 77:102387.

Hoch, Tobias; Schulz, Daniel; Eling, Nils; Gómez, Julia Martínez; Levesque, Mitchell P; Bodenmiller, Bernd (2022). Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology, 7(70):eabk1692.

Kaushik, Sandeep S; Bylun, Mikael; Cozzin, Cristina; Shanbhag, Dattesh; Petit, Steven F; Wyatt, Jonathan J; Menzel, Marion I; Pirkl, Carolin M; Mehta, Bhairav; Chauhan, Vikas; Chandrasekharan, Kesavadas; Jonsson, Jojakim; Nyholm, Tufve; Wiesinger, Florian; Menze, Bjoern H (2022). Region of Interest focused MRI to Synthetic CT Translation using Regression and Classification Multi-task Network. ArXiv.org 2203.16288, Cornell University.

Shit, Suprosanna; Koner, Rajat; Wittmann, Bastian; Paetzold, Johannes C; Ezhov, Ivan; Li, Hongwei; Pan, Jiazhen; Sharifzadeh, Sahand; Kaissis, Georgios; Tresp, Volker; Menze, Bjoern (2022). Relationformer: A Unified Framework for Image-to-Graph Generation. ArXiv.org 10202, Cornell University.

Avar, Merve; Heinzer, Daniel; Thackray, Alana M; Liu, Yingjun; Hruska-Plochan, Marian; Sellitto, Stefano; Schaper, Elke; Pease, Daniel Patrick; Yin, Jiang-An; Lakkaraju, Asvin K K; Emmenegger, Marc; Losa, Marco; Chincisan, Andra; Hornemann, Simone Alexandra; Polymenidou, Magdalini; Bujdoso, Raymond; Aguzzi, Adriano (2022). An Arrayed Genome-Wide Perturbation Screen Identifies the Ribonucleoprotein hnRNP K As Rate-Limiting for Prion Propagation. bioRxiv 482765, Cold Spring Harbor Laboratory.

Rehm, Karoline; Vollenweider, Vera; Kümmerli, Rolf; Bigler, Laurent (2022). A comprehensive method to elucidate pyoverdines produced by fluorescent Pseudomonas spp. by UHPLC-HR-MS/MS. Analytical and Bioanalytical Chemistry, 414(8):2671-2685.

Navarro, Fernando; Sasahara, Guido; Shit, Suprosanna; Ezhov, Ivan; Peeken, Jan C; Combs, Stephanie E; Menze, Bjoern H (2022). A unified 3D framework for Organs at Risk Localization and Segmentation for Radiation Therapy Planning. ArXiv.org 00624, Cornell University.

Biller-Andorno, Nikola; Ferrario, Andrea; Joebges, Susanne; Krones, Tanja; Massini, Federico; Barth, Phyllis; Arampatzis, Georgios; Krauthammer, Michael (2022). AI support for ethical decision-making around resuscitation: proceed with care. Journal of Medical Ethics, 48(3):175-183.

Rühling, Sebastian; Navarro, Fernando; Sekuboyina, Anjany; El Husseini, Malek; Baum, Thomas; Menze, Bjoern; Braren, Rickmer; Zimmer, Claus; Kirschke, Jan S (2022). Automated detection of the contrast phase in MDCT by an artificial neural network improves the accuracy of opportunistic bone mineral density measurements. European Radiology, 32(3):1465-1474.

Thomas, Marie Franziska; Kofler, Florian; Grundl, Lioba; Finck, Tom; Li, Hongwei; Zimmer, Claus; Menze, Björn; Wiestler, Benedikt (2022). Improving Automated Glioma Segmentation in Routine Clinical Use Through Artificial Intelligence-Based Replacement of Missing Sequences With Synthetic Magnetic Resonance Imaging Scans. Investigative Radiology, 57(3):187-193.

Lipková, Jana; Menze, Bjoern; Wiestler, Benedikt; Koumoutsakos, Petros; Lowengrub, John S (2022). Modelling glioma progression, mass effect and intracranial pressure in patient anatomy. Journal of the Royal Society Interface, 19(188):20210922.

Bost, Pierre; Schulz, Daniel; Engler, Stefanie; Wasserfall, Clive H; Bodenmiller, Bernd (2022). Optimizing multiplexed imaging experimental design through tissue spatial segregation estimation. bioRxiv 470262, Cold Spring Harbor Laboratory.

Bayat, Amirhossein; Pace, Danielle F; Sekuboyina, Anjany; Payer, Christian; Stern, Darko; Urschler, Martin; Kirschke, Jan S; Menze, Bjoern H (2022). Anatomy-Aware Inference of the 3D Standing Spine Posture from 2D Radiographs. Tomography, 8(1):479-496.

Wagner, Johanna; Masek, Markus; Jacobs, Andrea; Soneson, Charlotte; Sivapatham, Sujana; Damond, Nicolas; de Souza, Natalie; Robinson, Mark D; Bodenmiller, Bernd (2022). Mass cytometric and transcriptomic profiling of epithelial-mesenchymal transitions in human mammary cell lines. Scientific Data, 9:44-60.

Paetzold, Johannes C; McGinnis, Julian; Shit, Suprosanna; Ezhov, Ivan; Büschl, Paul; Prabhakar, Chinmay; Todorov, Mihail I; Sekuboyina, Anjany; Kaissis, Georgios; Ertürk, Ali; Günnemann, Stephan; Menze, Bjoern (2022). Whole Brain Vessel Graphs: A Dataset and Benchmark for Graph Learning and Neuroscience (VesselGraph). ArXiv.org 2108.13233, Cornell University.

Mitamura, Yasutaka; Schulz, Daniel; Oro, Saskia; Li, Nick; Kolm, Isabel; Lang, Claudia; Ziadlou, Reihane; Tan, Ge; Bodenmiller, Bernd; Steiger, Peter; Marzano, Angelo; de Prost, Nicolas; Caudin, Olivier; Levesque, Mitchell; Stoffel, Corinne; Schmid-Grendelmeier, Peter; Maverakis, Emanual; Akdis, Cezmi A; Brüggen, Marie-Charlotte (2022). Cutaneous and systemic hyperinflammation drives maculopapular drug exanthema in severely ill COVID-19 patients. Allergy, 77(2):595-608.

Gafita, Andrei; Wang, Hui; Robertson, Andrew; Armstrong, Wesley R; Zaum, Raphael; Weber, Manuel; Yagubbayli, Farid; Kratochwil, Clemens; Grogan, Tristan R; Nguyen, Kathleen; Navarro, Fernando; Esfandiari, Rouzbeh; Rauscher, Isabel; Menze, Bjoern; Elashoff, David; Delpassand, Ebrahim S; Herrmann, Ken; Czernin, Johannes; Hofman, Michael S; Calais, Jeremie; Fendler, Wolfgang P; Eiber, Matthias (2022). Tumor Sink Effect in 68Ga-PSMA-11 PET: Myth or Reality? Journal of Nuclear Medicine, 63(2):226-232.

Jambeau, Melanie; Meyer, Kevin Daniel; Hruska-Plochan, Marian; Tabet, Ricardos; Lee, Chao-Zong; Ray-Soni, Ananya; Aguilar, Corey; Savage, Kitty; Mishra, Nibha; Cavegn, Nicole; Borter, Petra; Lin, Chun-Chia; Jansen-West, Karen; Jiang, Jay; Freyermuth, Fernande; Li, Nan; De Rossi, Pierre; Pérez-Berlanga, Manuela; et al; Maniecka, Zuzanna; Weber, Julien; Kankel, Mark W; Rushe, Mia; Hock, Christoph; Nitsch, Roger M; Cleveland, Don W; Montrasio, Fabio; Grimm, Jan; Polymenidou, Magdalini (2022). Comprehensive preclinical evaluation of human-derived anti-poly-GA antibodies in cellular and animal models of C9ORF72 disease. bioRxiv 475329, Cold Spring Harbor Laboratory.

Mächler, Leon; Ezhov, Ivan; Kofler, Florian; Shit, Suprosanna; Paetzold, Johannes C; Loehr, Timo; Zimmer, Claus; Wiestler, Benedikt; Menze, Bjoern H (2022). FedCostWAvg: A New Averaging for Better Federated Learning. In: Crimi, Alessandro; Bakas, Spyridon. Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. Cham: Springer, 383-391.

Sahadevan, Sonu; Pérez-Berlanga, Manuela; Polymenidou, Magdalini (2022). Identification of RNA–RBP Interactions in Subcellular Compartments by CLIP-Seq. In: Matějů, Daniel; Chao, Jeffrey A. The Integrated Stress Response - Methods and Protocols. New York: Springer, 305-323.

Lüdke, David; Amiranashvili, Tamaz; Ambellan, Felix; Ezhov, Ivan; Menze, Bjoern H; Zachow, Stefan (2022). Landmark-Free Statistical Shape Modeling Via Neural Flow Deformations. In: Wang, Linwei; Dou, Qi; Fletcher, Thomas P; Speidel, Stefanie; Liu, Shuo. Medical Image Computing and Computer Assisted Intervention : MICCAI 2022. Cham: Springer, 453-463.

Hoces, Daniel; Corak, Basak; Estrada Brull, Anna; Berent, Sara; Faccin, Erica; Moresi, Claudia; Keys, Tim; Joller, Nicole; Slack, Emma (2022). Microbiota colonization tunes the antigen threshold of microbiota-specific T cell activation in the gut. bioRxiv 501979, Cold Spring Harbor Laboratory.

Figueiredo, Alexandre R T; Özkaya, Özhan; Kümmerli, Rolf; Kramer, Jos (2022). Siderophores drive invasion dynamics in bacterial communities through their dual role as public good versus public bad. Ecology Letters, 25(1):138-150.

Shlesinger, Danielle; Hong, Kai-Lin; Shammas, Ghazal; Page, Nicolas; Sandu, Ioana; Agrafiotis, Andreas; Kreiner, Victor; Vincenti, Ilena; Wagner, Ingrid; Piccinno, Margot; Mariotte, Alexandre; Klimek, Bogna; Dizerens, Raphael; Manero-Carranza, Marcos; Kuhn, Raphael; Ehling, Roy; Frei, Lester; Khodaverdi, Keywan; Panetti, Camilla; Joller, Nicole; Oxenius, Annette; Merkler, Doron; Reddy, Sai T; Yermanos, Alexander; Fonta, Nicolas (2022). Single-cell immune repertoire sequencing of B and T cells in murine models of infection and autoimmunity. bioRxiv 479381, Cold Spring Harbor Laboratory.

Pérez-Berlanga, Manuela; Wiersma, Vera; Zbinden, Aurélie; De Vos, Laura; Wagner, Ulrich; Foglieni, Chiara; Mallona Gonzalez, Izaskun; Betz, Katharina M; Cléry, Antoine; Weber, Julien; Guo, Zhongning; Rigort, Ruben; De Rossi, Pierre; Manglunia, Ruchi; Tantardini, Elena; Sahadevan, Sonu; Stach, Oliver; Hruska-Plochan, Marian; Allain, Frederic H-T; Paganetti, Paolo; Polymenidou, Magdalini (2022). TDP-43 oligomerization and RNA binding are codependent but their loss elicits distinct pathologies. bioRxiv PPR49, Cold Spring Harbor Laboratory.

Iqbal, Jeffrey David; Krauthammer, Michael; Biller-Andorno, Nikola (2022). The Use and Ethics of Digital Twins in Medicine. Journal of Law, Medicine & Ethics, 50(3):583-596.

Kuett, Laura; Catena, Raúl; Özcan, Alaz; Plüss, Alex; Schraml, Peter; Moch, Holger; de Souza, Natalie; Bodenmiller, Bernd; Cancer Grand Challenges IMAXT Consortium (2022). Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment. Nature Cancer, 3(1):122-133.

Fujimoto, Koji; Nishio, Mizuho; Sugiyama, Osamu; Ichikawa, Kana; Cornelius, Joseph; Lithgow-Serrano, Oscar; Kanjirangat, Vani; Rinaldi, Fabio; Horvath, Aron N; Nooralahzadeh, Farhad; Krauthammer, Michael (2022). Approach for Named Entity Recognition and Case Identification Implemented by ZuKyo-JA Sub-team at the NTCIR-16 Real-MedNLP Task. In: NTCIR 16 Conference: Proceedings of the 16th NTCIR Conference on Evaluation of Information Access Technologies, Tokyo, Japan, 14 June 2022 - 17 June 2022, 322-329.

Heiliger, Lars; Sekuboyina, Anjany; Menze, Bjoern; Egger, Jan; Kleesiek, Jens (2022). Beyond Medical Imaging - A Review of Multimodal Deep Learning in Radiology. TechRxiv 19103432, University of Zurich.

Schwarz, Kyriakos; Pliego-Mendieta, Alicia; Planas-Plaz, Lara; Pauli, Chantal; Allam, Ahmed; Krauthammer, Michael (2022). DDoS: A Graph Neural Network based Drug Synergy Prediction Algorithm. ArXiv.org 2210.00802, Cornell University.

Cornelius, Joseph; Lithgow-Serrano, Oscar; Kanjirangat, Vani; Rinaldi, Fabio; Fujimoto, Koji; Nishio, Mizuho; Sugiyama, Osamu; Ichikawa, Kana; Nooralahzadeh, Farhad; Horvath, Aron N; Krauthammer, Michael (2022). Leveraging Token-Based Concept Information and Data Augmentation in Few-Resource NER: ZuKyo-EN at the NTCIR-16 Real-MedNLP task. In: NTCIR 16 Conference: Proceedings of the 16th NTCIR Conference on Evaluation of Information Access Technologies, Tokyo, Japan, 14 June 2022 - 17 June 2022, NTCIR.

Windhager, Jonas. Multiplexed tissue image processing and spatial single-cell data integration. 2022, University of Zurich, Faculty of Science.

Bonvin, Raphaël; Buhmann, Joachim; Cotrini Jimenez, Carlos; Egger, Marcel; Geissler, Alexander; Krauthammer, Michael; Schirlo, Christian; Spiess, Christiane; Steurer, J; Vokinger, Kerstin N; Vogt, Julia. Neue Lernziele für das Medizinstudium erarbeitet. In: Neue Lernziele für das Medizinstudium erarbeitet, 2022, 98-101.

Liu, Hailing; Zhao, Yu; Yang, Fan; Lou, Xiaoying; Wu, Feng; Li, Hang; Xing, Xiaohan; Peng, Tingying; Menze, Bjoern; Huang, Junzhou; Zhang, Shujun; Han, Anjia; Yao, Jianhua; Fan, Xinjuan (2022). Preoperative Prediction of Lymph Node Metastasis in Colorectal Cancer with Deep Learning. BME Frontiers, 2022:9860179.

Pérez Berlanga, Manuela; Berlanga, Manuela Pérez. Roles of TDP-43 oligomerization and RNA binding in physiology and pathology. 2022, University of Zurich, Faculty of Science.

Kuett, Laura. Studying breast cancer invasion and metastasis with 2D and 3D imaging mass cytometry. 2022, University of Zurich, Faculty of Science.

2021

Kofler, Florian; Ezhov, Ivan; Fidon, Lucas; Pirkl, Carolin M; Paetzold, Johannes C; Burian, Egon; Pati, Sarthak; El Husseini, Malek; Navarro, Fernando; Shit, Suprosanna; Kirschke, Jan; Bakas, Spyridon; Zimmer, Claus; Wiestler, Benedikt; Menze, Bjoern H (2021). Robust, Primitive, and Unsupervised Quality Estimation for Segmentation Ensembles. Frontiers in Neuroscience, 15:752780.

Kramer, Jos; Kümmerli, Rolf (2021). Losing out to improve group fitness. eLife, 10:e75243.

Zhylka, Andrey; Sollmann, Nico; Kofler, Florian; Radwan, Ahmed; De Luca, Alberto; Gempt, Jens; Wiestler, Benedikt; Menze, Bjoern; Krieg, Sandro M; Zimmer, Claus; Kirschke, Jan S; Sunaert, Stefan; Leemans, Alexander; Pluim, Josien P W (2021). Tracking the Corticospinal Tract in Patients With High-Grade Glioma: Clinical Evaluation of Multi-Level Fiber Tracking and Comparison to Conventional Deterministic Approaches. Frontiers in Oncology, 11:761169.

Endt, Sebastian; Pirkl, Carolin M; Verdun, Claudio M; Menze, Bjoern H; Menzel, Marion I (2021). Unmixing tissue compartments via deep learning T1-T2-relaxation correlation imaging. In: Seventeenth International Symposium on Medical Information Processing and Analysis, Campinas, Brazil, 17 November 2021 - 19 November 2021. SPIE, 120880P.

De Rossi, Pierre; Lewis, Amanda J; Furrer, Johanna; De Vos, Laura; Demeter, Tomas; Zbinden, Aurélie; Zhong, Weijia; Wiersma, Vera I; Scialo, Carlo; Weber, Julien; Guo, Zhongning; Scaramuzza, Stefano; Di Fabrizio, Marta; Böing, Carolin; Castaño‐Díez, Daniel; Al‐Amoudi, Ashraf; Pérez-Berlanga, Manuela; Lashley, Tammaryn; Stahlberg, Henning; Polymenidou, Magdalini (2021). FTLD‐TDP assemblies seed neoaggregates with subtype‐specific features via a prion‐like cascade. EMBO Reports, 22(12):e53877.

Allam, Ahmed; Feuerriegel, Stefan; Rebhan, Michael; Krauthammer, Michael (2021). Analyzing Patient Trajectories With Artificial Intelligence. Journal of Medical Internet Research, 23(12):e29812.

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.

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.

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.

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.

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.

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.

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

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.

Rathmes, Giulia; Krauthammer, Michael (2021). Künstliche Intelligenz in der Medizin : Chancen und Risiken der KI. Hausarzt Praxis, 16(11):6-10.

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.

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.

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.

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.

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.

Wiersma, Vera I; Polymenidou, Magdalini (2021). Sharing is caring: The benefits of distributing protein aggregates among microglial networks. Neuron, 109(20):3228-3230.

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.

Li, Jianning; Pimentel, Pedro; Szengel, Angelika; Ehlke, Moritz; Lamecker, Hans; Zachow, Stefan; Estacio, Laura; Doenitz, Christian; Ramm, Heiko; Shi, Haochen; Chen, Xiaojun; Matzkin, Franco; Newcombe, Virginia; Ferrante, Enzo; Jin, Yuan; Ellis, David G; Aizenberg, Michele R; Kodym, Oldrich; Spanel, Michal; Herout, Adam; Mainprize, James G; Fishman, Zachary; Hardisty, Michael R; Bayat, Amirhossein; Shit, Suprosanna; Wang, Bomin; Liu, Zhi; Eder, Matthias; Pepe, Antonio; Gsaxner, Christina; et al (2021). AutoImplant 2020-First MICCAI Challenge on Automatic Cranial Implant Design. IEEE Transactions on Medical Imaging, 40(9):2329-2342.

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.

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.

Guo, Rui; Hu, Xiaobin; Song, Haoming; Xu, Pengpeng; Xu, Haoping; Rominger, Axel; Lin, Xiaozhu; Menze, Bjoern; Li, Biao; Shi, Kuangyu (2021). Weakly supervised deep learning for determining the prognostic value of 18F-FDG PET/CT in extranodal natural killer/T cell lymphoma, nasal type. European Journal of Nuclear Medicine and Molecular Imaging, 48(10):3151-3161.

Niggli, Selina; Wechsler, Tobias; Kümmerli, Rolf (2021). Single-Cell Imaging Reveals That Staphylococcus aureus Is Highly Competitive Against Pseudomonas aeruginosa on Surfaces. Frontiers in Cellular and Infection Microbiology, 11:733991.

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.

Butaitė, Elena; Kramer, Jos; Kümmerli, Rolf (2021). Local adaptation, geographical distance and phylogenetic relatedness: Assessing the drivers of siderophore‐mediated social interactions in natural bacterial communities. Journal of Evolutionary Biology, 34(8):1266-1278.

Hiller, Helmut; Beachy, Dawn E; Lebowitz, Joseph J; Engler, Stefanie; Mason, Justin R; Miller, Douglas R; Kusmarteva, Irina; Jacobsen, Laura M; Posgai, Amanda L; Khoshbouei, Habibeh; Oram, Richard A; Schatz, Desmond A; Hattersley, Andrew T; Bodenmiller, Bernd; Atkinson, Mark A; Nick, Harry S; Wasserfall, Clive H (2021). Monogenic Diabetes and Integrated Stress Response Genes Display Altered Gene Expression in Type 1 Diabetes. Diabetes, 70(8):1885-1897.

Lu, Junyan; Cannizzaro, Ester; Meier-Abt, Fabienne; Scheinost, Sebastian; Bruch, Peter-Martin; Giles, Holly A R; Lütge, Almut; Hüllein, Jennifer; Wagner, Lena; Giacopelli, Brian; Nadeu, Ferran; Delgado, Julio; Campo, Elías; Mangolini, Maurizio; Ringshausen, Ingo; Böttcher, Martin; Mougiakakos, Dimitrios; Jacobs, Andrea; Bodenmiller, Bernd; Dietrich, Sascha; Oakes, Christopher C; Zenz, Thorsten; Huber, Wolfgang (2021). Multi-omics reveals clinically relevant proliferative drive associated with mTOR-MYC-OXPHOS activity in chronic lymphocytic leukemia. Nature cancer, 2(8):853-864.

Hoch, Tobias; Schulz, Daniel; Eling, Nils; Gómez, Julia Martínez; Levesque, Mitchell P; Bodenmiller, Bernd (2021). Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. bioRxiv 454093, Cold Spring Harbor Laboratory.

Emmenegger, Marc; De Cecco, Elena; Hruska‐Plochan, Marian; Eninger, Timo; Schneider, Matthias M; Barth, Melanie; Tantardini, Elena; de Rossi, Pierre; Bacioglu, Mehtap; Langston, Rebekah G; Kaganovich, Alice; Bengoa‐Vergniory, Nora; Gonzalez‐Guerra, Andrès; Avar, Merve; Heinzer, Daniel; Reimann, Regina; Häsler, Lisa M; Herling, Therese W; Matharu, Naunehal S; Landeck, Natalie; Luk, Kelvin; Melki, Ronald; Kahle, Philipp J; Hornemann, Simone; Knowles, Tuomas P J; Cookson, Mark R; Polymenidou, Magdalini; Jucker, Mathias; Aguzzi, Adriano (2021). LAG3 is not expressed in human and murine neurons and does not modulate α‐synucleinopathies. EMBO Molecular Medicine:e 14745.

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.

Bressan, Dario; Mulvey, Claire M; Qosaj, Fatime; Becker, Robert; Grimaldi, Flaminia; Coffey, Suvi; Vogl, Sara Lisa; Kuett, Laura; Catena, Raul; Dariush, Ali; Gonzalez-Fernandez, Carlos; Gonzalez-Solares, Eduardo A; Sa’d, Mohammad Al; Yoldaş, Aybüke Küpcü; Whitmarsh, Tristan; Falciatori, Ilaria; Watson, Spencer S; Joyce, Johanna A; Walton, Nicholas; Bodenmiller, Bernd; Harris, Owen; Hannon, Gregory J (2021). Exploration and analysis of molecularly annotated, 3D models of breast cancer at single-cell resolution using virtual reality. bioRxiv 448342, Cold Spring Harbor Laboratory.

Navarro, Fernando; Dapper, Hendrik; Asadpour, Rebecca; Knebel, Carolin; Spraker, Matthew B; Schwarze, Vincent; Schaub, Stephanie K; Mayr, Nina A; Specht, Katja; Woodruff, Henry C; Lambin, Philippe; Gersing, Alexandra S; Nyflot, Matthew J; Menze, Bjoern H; Combs, Stephanie E; Peeken, Jan C (2021). Development and External Validation of Deep-Learning-Based Tumor Grading Models in Soft-Tissue Sarcoma Patients Using MR Imaging. Cancers, 13(12):2866.

Navarro, Fernando; Watanabe, Christopher; Shit, Suprosanna; Sekuboyina, Anjany; Peeken, Jan C; Combs, Stephanie E; Menze, Bjoern H (2021). Evaluating the Robustness of Self-Supervised Learning in Medical Imaging. ArXiv.org 2105.06986, Cornell University.

Tognetti, Marco; Gabor, Attila; Yang, Mi; Cappelletti, Valentina; Windhager, Jonas; Rueda, Oscar M; Charmpi, Konstantina; Esmaeilishirazifard, Elham; Bruna, Alejandra; de Souza, Natalie; Caldas, Carlos; Beyer, Andreas; Picotti, Paola; Saez-Rodriguez, Julio; Bodenmiller, Bernd (2021). Deciphering the signaling network of breast cancer improves drug sensitivity prediction. Cell Systems, 12(5):401-418.e12.

González, Jaime; Salvador, Manuel; Özkaya, Özhan; Spick, Matt; Reid, Kate; Costa, Catia; Bailey, Melanie J; Avignone Rossa, Claudio; Kümmerli, Rolf; Jiménez, José I (2021). Loss of a pyoverdine secondary receptor in Pseudomonas aeruginosa results in a fitter strain suitable for population invasion. The ISME journal, 15(5):1330-1343.

Horvath, Izabela; Paetzold, Johannes C; Schoppe, Oliver; Al-Maskari, Rami; Ezhov, Ivan; Shit, Suprosanna; Li, Hongwei; Ertuerk, Ali; Menze, Bjoern (2021). METGAN: Generative Tumour Inpainting and Modality Synthesis in Light Sheet Microscopy. ArXiv.org 10993, Cornell University.

Li, Hongwei; Prasad, Rameshwara G N; Sekuboyina, Anjany; Niu, Chen; Bai, Siwei; Hemmert, Werner; Menze, Bjoern (2021). Micro-Ct Synthesis and Inner Ear Super Resolution via Generative Adversarial Networks and Bayesian Inference. In: 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI), Nice, France, 13 April 2021 - 16 April 2021. Institute of Electrical and Electronics Engineers, online.

Eling, Nils; Damond, Nicolas; Hoch, Tobias; Bodenmiller, Bernd (2021). Cytomapper: an R/bioconductor package for visualisation of highly multiplexed imaging data. Bioinformatics, 36(24):5706-5708.

Golbabaee, Mohammad; Buonincontri, Guido; Pirkl, Carolin M; Menzel, Marion I; Menze, Bjoern H; Davies, Mike; Gómez, Pedro A (2021). Compressive MRI quantification using convex spatiotemporal priors and deep encoder-decoder networks. Medical Image Analysis, 69:101945.

Jayakumar, Priyanikha; Thomas, Stephen A; Brown, Sam P; Kümmerli, Rolf (2021). Pseudomonas aeruginosa reaches collective decisions via transient segregation of quorum sensing activities across cells. bioRxiv 436499, Cold Spring Harbor Laboratory.

Kofler, Florian; Ezhov, Ivan; Isensee, Fabian; Balsiger, Fabian; Berger, Christoph; Koerner, Maximilian; Paetzold, Johannes C; Li, Hongwei; Shit, Suprosanna; McKinley, Richard; Spyridon, Bakas; Zimmer, Claus; Ankerst, Donna; Kirschke, Jan S; Wiestler, Benedikt; Menze, Bjoern (2021). Are we using appropriate segmentation metrics? Identifying correlates of human expert perception for CNN training beyond rolling the DICE coefficient. ArXiv.org 2103.06205, Cornell University.

Menze, Bjoern; Isensee, Fabian; Wiest, Roland; Wiestler, Bene; Maier-Hein, Klaus; Reyes, Mauricio; Bakas, Spyridon (2021). Analyzing magnetic resonance imaging data from glioma patients using deep learning. Computerized Medical Imaging and Graphics, 88:101828.

El‐Rewaidy, Hossam; Fahmy, Ahmed S; Pashakhanloo, Farhad; Cai, Xiaoying; Kucukseymen, Selcuk; Csecs, Ibolya; Neisius, Ulf; Haji‐Valizadeh, Hassan; Menze, Bjoern; Nezafat, Reza (2021). Multi‐domain convolutional neural network (MD‐CNN) for radial reconstruction of dynamic cardiac MRI. Magnetic Resonance in Medicine, 85(3):1195-1208.

Ramelyte, Egle; Tastanova, Aizhan; Balázs, Zsolt; Ignatova, Desislava; Turko, Patrick; Menzel, Ulrike; Guenova, Emmanuella; Beisel, Christian; Krauthammer, Michael; Levesque, Mitchell Paul; Dummer, Reinhard (2021). Oncolytic virotherapy-mediated anti-tumor response: a single-cell perspective. Cancer Cell, 39(3):394-406.e4.

Irmisch, Anja; Bonilla, Ximena; Chevrier, Stéphane; Lehmann, Kjong-Van; Singer, Franziska; Toussaint, Nora C; Esposito, Cinzia; Mena, Julien; Milani, Emanuela S; Casanova, Ruben; Stekhoven, Daniel J; Wegmann, Rebekka; Jacob, Francis; Sobottka-Brillout, Bettina; Goetze, Sandra; Kuipers, Jack; Sarabia del Castillo, Jacobo; Prummer, Michael; Tuncel, Mustafa A; Menzel, Ulrike; Jacobs, Andrea; Engler, Stefanie; Sivapatham, Sujana; Frei, Anja L; Gut, Gabriele; Ficek, Joanna; Miglino, Nicola; Aebersold, Rudolf; Bacac, Marina; Beerenwinkel, Niko; Moch, Holger; Beisel, Christian; Bodenmiller, Bernd; Dummer, Reinhard; Heinzelmann-Schwarz, Viola; Koelzer, Viktor H; Manz, Markus G; Pelkmans, Lucas; Snijder, Berend; Theocharides, Alexandre P A; Tolnay, Markus; Wicki, Andreas; Wollscheid, Bernd; Rätsch, Gunnar; Levesque, Mitchell Paul (2021). The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support. Cancer Cell, 39(3):288-293.

Wennmann, Markus; Hielscher, Thomas; Kintzelé, Laurent; Menze, Bjoern H; Langs, Georg; Merz, Maximilian; Sauer, Sandra; Kauczor, Hans-Ulrich; Schlemmer, Heinz-Peter; Delorme, Stefan; Goldschmidt, Hartmut; Weinhold, Niels; Hillengass, Jens; Weber, Marc-André (2021). Analyzing Longitudinal wb-MRI Data and Clinical Course in a Cohort of Former Smoldering Multiple Myeloma Patients: Connections between MRI Findings and Clinical Progression Patterns. Cancers, 13(5):961.

Dong, Xingchen; Li, Hongwei; Jiang, Zhutong; Grünleitner, Theresa; Güler, İnci; Dong, Jie; Wang, Kun; Köhler, Michael H; Jakobi, Martin; Menze, Bjoern H; Yetisen, Ali K; Sharp, Ian D; Stier, Andreas V; Finley, Jonathan J; Koch, Alexander W (2021). 3D Deep Learning Enables Accurate Layer Mapping of 2D Materials. ACS Nano, 15(2):3139-3151.

Hu, Xiaobin; Zhao, Yu; Sekuboyina, Anjany; Menze, Bjoern (2021). Multi-Texture GAN: Exploring the Multi-Scale Texture Translation for Brain MR Images. ArXiv.org 2102.07225, Cornell University.

Alvarado-Cruz, Isabel; Mahmoud, Mariam; Khan, Mohammed; Zhao, Shilin; Oeck, Sebastian; Meas, Rithy; Clairmont, Kaylyn; Quintana, Victoria; Zhu, Ying; Porciuncula, Angelo; Wyatt, Hailey; Ma, Shuangge; Shyr, Yu; Kong, Yong; LoRusso, Patricia M; Laverty, Daniel; Nagel, Zachary D; Schalper, Kurt A; Krauthammer, Michael; Sweasy, Joann B (2021). Differential immunomodulatory effect of PARP inhibition in BRCA1 deficient and competent tumor cells. Biochemical Pharmacology, 184:114359.

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.

Konrad, Sebastian F; Vanderlinden, Willem; Frederickx, Wout; Brouns, Tine; Menze, Björn H; De Feyter, Steven; Lipfert, Jan (2021). High-throughput AFM analysis reveals unwrapping pathways of H3 and CENP-A nucleosomes. Nanoscale, 13(10):5435-5447.

Li, Hongwei; Xue, Fei-Fei; Chaitanya, Krishna; Luo, Shengda; Ezhov, Ivan; Wiestler, Benedikt; Zhang, Jianguo; Menze, Bjoern (2021). Imbalance-Aware Self-supervised Learning for 3D Radiomic Representations. In: de Buijne, Marleen; Cotin, Stéphane; Speidel, Stefanie; Zhen, Yefeng; Essert, Caroline. Medical Immage Computing and Computer Assisted Intervention - MICCAI 2021. Strasbourg: Springer, 36-46.

Shit, Suprosanna; Das, Dhritiman; Ezhov, Ivan; Paetzold, Johannes C; Sanches, Augusto F; Thuerey, Nils; Menze, Bjoern H (2021). Velocity-To-Pressure (V2P) - Net: Inferring Relative Pressures from Time-Varying 3D Fluid Flow Velocities. In: Feragen, Aasa; Sommer, Stefan; Schnabel, J; Nielsen, Mads. Information Processing in Medical Imaging. Cham: Springer, 545-558.

Schwarz, Kyriakos; Allam, Ahmed; Perez Gonzalez, Nicolas Andres; Krauthammer, Michael (2021). AttentionDDI: Siamese attention‑based deep learning method for drug–drug interaction predictions. BMC Bioinformatics, 22(1):412.

Shit, Suprosanna; Ezhov, Ivan; Paetzold, Johannes C; Menze, Bjoern (2021). Aν-Net: Automatic Detection and Segmentation of Aneurysm. In: Hennemuth, A. Cerebral Aneurysm Detection and Analysis. Cham: Springer, 51-57.

Ma, Jiechao; Li, Xiang; Li, Hongwei; Wang, Ruixuan; Menze, Bjoern; Zheng, Wei-Shi (2021). Cross-View Relation Networks for Mammogram Mass Detection. International Conference on Pattern Recognition:Epub ahead of print.

Mridha, Subham. Ecology and Evolution of Bacterial Social Behaviours in Phenotypically Heterogenous Populations. 2021, University of Zurich, Faculty of Science.

Niggli, Selina. Ecology and Evolution of Interspecies Interactions between Pseudomonas aeruginosa and Staphylococcus aureus. 2021, University of Zurich, Faculty of Science.

Fischer, Jana Raja. High-dimensional profiling of the breast cancer microarchitecture. 2021, University of Zurich, Faculty of Science.

Tietscher, Sandra. Single-cell profiling of the tumor immune microenvironment of primary and metastatic human breast cancer. 2021, University of Zurich, Faculty of Science.

Figueiredo, Alexandre R T. The Ecology and Evolution of Bacterial Social Interactions and How They Shape Microbial Communities and Interactions with Hosts. 2021, University of Zurich, Faculty of Science.

2020

Wiestler, Benedikt; Menze, Bjoern (2020). Deep learning for medical image analysis: a brief introduction. Neuro-oncology advances, 2(Supplement):iv35-iv41.

Tetteh, Giles; Efremov, Velizar; Forkert, Nils D; Schneider, Matthias; Kirschke, Jan; Weber, Bruno; Zimmer, Claus; Piraud, Marie; Menze, Björn H (2020). DeepVesselNet: Vessel Segmentation, Centerline Prediction, and Bifurcation Detection in 3-D Angiographic Volumes. Frontiers in Neuroscience, 14:592352.

Kinkead, Laura; Allam, Ahmed; Krauthammer, Michael (2020). AutoDiscern: rating the quality of online health information with hierarchical encoder attention-based neural networks. BMC Medical Informatics and Decision Making, 20:104.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Polymenidou, Magdalini (2020). A Gut Feeling about C9ORF72. Trends in Immunology, 41(9):755-757.

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.

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.

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.

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..

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.

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.

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.

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.

Figueiredo, Alexandre R T; Kramer, Jos (2020). Cooperation and Conflict Within the Microbiota and Their Effects On Animal Hosts. Frontiers in Ecology and Evolution, 8:132.

Lun, Xiao-Kang; Bodenmiller, Bernd (2020). Profiling Cell Signaling Networks at Single-cell Resolution. Molecular & Cellular Proteomics, 19(5):744-756.

Rost, Felix. Memory Formation and Functional Specialization of Regulatory T Cells in TH1-polarized Immune Responses. 2020, University of Zurich, Faculty of Science.

Kramer, Jos; Özkaya, Özhan; Kümmerli, Rolf (2020). Bacterial siderophores in community and host interactions. Nature Reviews. Microbiology, 18(3):152-163.

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.

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.

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.

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.

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.

Hembach, Katharina M. Computational Analyses of High-Throughput Sequencing Data to Understand RNA Metabolism Defects Associated with ALS. 2020, University of Zurich, Faculty of Science.

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.

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.

Mala Kkoth, Sonu Sahadevan. Understanding the Role of FUS in Synaptic RNA Homeostasis and its Misregulation in Neurodegenerative Diseases. 2020, University of Zurich, Faculty of Science.

2019

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.

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.

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.

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.

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.

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.

Krauthammer, Michael. Mobile Health – Eine Technologie wird erwachsen. In: readme : Das Bulletin derUZH Alumni Informatik, 41, 1 September 2019, 3-5.

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.

Schorer, Michelle. The Role of The Co-inhibitory Receptor TIGIT During Viral Infections. 2019, University of Zurich, Faculty of Science.

Jambeau, Melanie. Understanding and Targeting Dipeptide Repeat Protein Toxicity by Immunotherapy in ALS and FTD. 2019, University of Zurich, Faculty of Science.

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.

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.

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.

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.

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.

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.

Rakebrandt, Nikolas Jan. Responses of CD4+ T Helper Cells and Regulatory T Cells During Heterologous Immune Challenge. 2019, University of Zurich, Faculty of Science.

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.

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.

Manuela, Pérez-Berlanga; Florent, Laferrière; Magdalini, Polymenidou (2019). SarkoSpin: A Technique for Biochemical Isolation and Characterization of Pathological TDP-43 Aggregates. Bio-protocol, 9(22):1-10.

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.

Rezzoagli, Chiara. Bacterial cooperation and the design of evolutionary robust antimicrobials. 2019, University of Zurich, Faculty of Science.

Tognetti, Marco. Deciphering the Signaling Network Landscape of Breast Cancer Supports Precision Medicine. 2019, University of Zurich, Faculty of Science.

Bellini, Elisa. Identification of molecular pathways involved in endometrial cancer progression. 2019, University of Zurich, Faculty of Science.

Zanotelli, Vito R T. Investigation of intra- and intercellular signaling through mass cytometry based single cell methods. 2019, University of Zurich, Faculty of Science.

Wagner-Albrecht, Johanna. Single-cell proteomic characterization of the tumor and immune ecosystem of human breast cancer with focus on metastatic potential. 2019, University of Zurich, Faculty of Science.

Foglieni, Chiara. Split GFP Technologies to Study Structural and Functional Biomolecular Interactions in Cells: Analysis of TDP-43 Physiological Oligomers. 2019, University of Zurich, Faculty of Science.

2018

Boersema, Paul J; Melnik, Andre; Hazenberg, Bouke P C; Rezeli, Melinda; Marko-Varga, György; Kamiie, Junichi; Portelius, Erik; Blennow, Kaj; Zubarev, Roman A; Polymenidou, Magdalini; Picotti, Paola (2018). Biology/Disease-Driven Initiative on Protein-Aggregation Diseases of the Human Proteome Project: Goals and Progress to Date. Journal of Proteome Research, 17(12):4072-4084.

Jawaid, Ali; Khan, Romesa; Polymenidou, Magdalini; Schulz, Paul E (2018). Disease-modifying effects of metabolic perturbations in ALS/FTLD. Molecular Neurodegeneration, 13(1):63.

Hock, Eva-Maria; Maniecka, Zuzanna; Hruska-Plochan, Marian; Reber, Stefan; Laferrière, Florent; Sahadevan M.K., Sonu; Ederle, Helena; Gittings, Lauren; Pelkmans, Lucas; Dupuis, Luc; Lashley, Tammaryn; Ruepp, Marc-David; Dormann, Dorothee; Polymenidou, Magdalini (2018). Hypertonic Stress Causes Cytoplasmic Translocation of Neuronal, but Not Astrocytic, FUS due to Impaired Transportin Function. Cell Reports, 24(4):987-1000.e7.

Polymenidou, Magdalini (2018). The RNA face of phase separation. Science, 360(6391):859-860.

Arnol, Damien; Schapiro, Denis; Bodenmiller, Bernd; Saez-Rodriguez, Julio; Stegle, Oliver (2018). Modelling cell-cell interactions from spatial molecular data with spatial variance component analysis. bioRxiv 265256v3, Cold Spring Harbor Laboratory.

Maniecka, Zuzanna. Physiological and pathological TDP-43 assemblies and new ALS/FTD neuronal models. 2018, University of Zurich, Faculty of Science.

Lun, Xiaokang. Single-cell analysis reveals protein abundance-dependent signaling network modulations. 2018, University of Zurich, Faculty of Science.

2017

Regev, Aviv; Teichmann, Sarah A; Lander, Eric S; Amit, Ido; Benoist, Christophe; Birney, Ewan; Bodenmiller, Bernd; et al (2017). The Human Cell Atlas. eLife, 6:e27041.

Polymenidou, Magdalini; Cleveland, Don W (2017). Biological Spectrum of Amyotrophic Lateral Sclerosis Prions. Cold Spring Harbor Perspectives in Medicine, 7(11):a024133.

Afroz, Tariq; Hock, Eva-Maria; Ernst, Patrick; Foglieni, Chiara; Jambeau, Melanie; Gilhespy, Larissa A B; Laferriere, Florent; Maniecka, Zuzanna; Plückthun, Andreas; Mittl, Peer; Paganetti, Paolo; Allain, Frédéric H T; Polymenidou, Magdalini (2017). Functional and dynamic polymerization of the ALS-linked protein TDP-43 antagonizes its pathologic aggregation. Nature Communications, 8:45.

Leske, Henning; Hornemann, Simone; Herrmann, Uli Simon; Zhu, Caihong; Dametto, Paolo; Li, Bei; Laferriere, Florent; Polymenidou, Magdalini; Pelczar, Pawel; Reimann, Regina Rose; Schwarz, Petra; Rushing, Elisabeth Jane; Wüthrich, Kurt; Aguzzi, Adriano (2017). Protease resistance of infectious prions is suppressed by removal of a single atom in the cellular prion protein. PLoS ONE, 12(2):e0170503.

2015

The Cancer Genome Atlas Network (2015). Genomic Classification of Cutaneous Melanoma. Cell, 161(7):1681-1696.

1995

Van de Voorde, A; Tytgat, J (1995). Transmembrane segments critical for potassium channel function. Biochemical and Biophysical Research Communications, 209(3):1094-101.

This list was generated on Wed Apr 24 23:20:53 2024 CEST.