Bernd Bodenmiller

ZORA Publication List

Publications

• Wegmann, Rebekka; Bonilla, Ximena; Casanova, Ruben; Chevrier, Stéphane; Coelho, Ricardo; Esposito, Cinzia; Ficek-Pascual, Joanna; Goetze, Sandra; Gut, Gabriele; Jacob, Francis; Jacobs, Andrea; Kuipers, Jack; Lischetti, Ulrike; Mena, Julien; Milani, Emanuela S; Prummer, Michael; Del Castillo, Jacobo Sarabia; Singer, Franziska; Sivapatham, Sujana; Toussaint, Nora C; Vilinovszki, Oliver; Wildschut, Mattheus H E; Thavayogarajah, Tharshika; Malani, Disha; TumorProfiler Consortium; et al; Aebersold, Rudolf; Bacac, Marina; Beerenwinkel, Niko; Beisel, Christian; Bodenmiller, Bernd (2024). Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia. Nature Communications, 15(1):9402.
• Kuett, Laura; Bollhagen, Alina; Tietscher, Sandra; Sobottka, Bettina; Eling, Nils; Varga, Zsuzsanna; Moch, Holger; de Souza, Natalie; Bodenmiller, Bernd (2024). Distant Metastases of Breast Cancer Resemble Primary Tumors in Cancer Cell Composition but Differ in Immune Cell Phenotypes. Cancer Research:Epub ahead of print.
• Immer, Alexander; Stark, Stefan G; Jacob, Francis; Bonilla, Ximena; Thomas, Tinu; Kahles, André; Goetze, Sandra; Milani, Emanuela S; Wollscheid, Bernd; Aebersold, Rudolf; Ak, Melike; Al-Quaddoomi, Faisal S; Albert, Silvana I; Albinus, Jonas; Alborelli, Ilaria; Andani, Sonali; Attinger, Per-Olof; Bacac, Marina; Baumhoer, Daniel; Beck-Schimmer, Beatrice; Beerenwinkel, Niko; Beisel, Christian; Bernasconi, Lara; Bertolini, Anne; Bodenmiller, Bernd; Bonilla, Ximena; Bosshard, Lars; Calgua, Byron; Casanova, Ruben; et al; Pelkmans, Lucas (2024). Probabilistic pathway-based multimodal factor analysis. Bioinformatics, 40(Suppl 1):i189-i198.
• de Souza, Natalie; Zhao, Shan; Bodenmiller, Bernd (2024). Multiplex protein imaging in tumour biology. Nature Reviews Cancer, 24(3):171-191.
• 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.
• 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.
• 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.
• 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.
• 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 (2023). Acquired resistance to anti-PD1 therapy in patients with NSCLC associates with immunosuppressive T cell phenotype. Nature Communications, 14(1):5154.
• 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.
• 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.
• 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.
• Andani, Sonali; Chen, Boqi; Ficek-Pascual, Joanna; Heinke, Simon; Casanova, Ruben; Sobottka, Bettina; Bodenmiller, Bernd; Koelzer, Viktor; Ratsch, Gunnar (2023). Multi-V-Stain: Multiplexed Virtual Staining of Histopathology Whole-Slide Images. In: Deep Generative Models for Health Workshop NeurIPS 2023, New Orleans, Louisiana, United States, 15 December 2023.
• Wild, Sophia A; Cannell, Ian G; Nicholls, Ashley; Kania, Katarzyn; Bressan, Dario; Hannon, Gregory J; Sawicka, Kirsty; Bodenmiller, Bernd (2022). Clonal transcriptomics identifies mechanisms of chemoresistance and empowers rational design of combination therapies. eLife, 11:e80981.
• Wang, Jian; Weiss, Tobias; Neidert, Marian C; Toussaint, Nora C; Naghavian, Reza; Moreno Sellés, Carla; Foege, Magdalena; Tomas Ojer, Paula; Medici, Gioele; Jelcic, Ivan; Schulz, Daniel; Rushing, Elisabeth; Dettwiler, Susanne; Schrörs, Barbara; Shin, Joo Heon; McKay, Ron; Wu, Catherine J; Lutterotti, Andreas; Sospedra, Mireia; Moch, Holger; Greiner, Erich F; Bodenmiller, Bernd; Regli, Luca; Weller, Michael; Roth, Patrick; Martin, Roland (2022). Vaccination with designed neopeptides induces intratumoral, cross-reactive CD4+ T cell responses in glioblastoma. Clinical Cancer Research, 28(24):5368-5382.
• Funnell, Tyler; Bodenmiller, Bernd (2022). Single-cell genomic variation induced by mutational processes in cancer. Nature, 612(7938):106-115.
• Martinelli, Adriano Luca; Wagner, Johanna; Bodenmiller, Bernd; Rapsomaniki, Maria Anna (2022). scQUEST: Quantifying tumor ecosystem heterogeneity from mass or flow cytometry data. STAR Protocols, 3(3):101578.
• Taeschler, Patrick; Adamo, Sarah; Deng, Yun; Cervia, Carlo; Zurbuchen, Yves; Chevrier, Stéphane; Raeber, Miro E; Hasler, Sara; Bächli, Esther; Rudiger, Alain; Stüssi-Helbling, Melina; Huber, Lars C; Bodenmiller, Bernd; Boyman, Onur; Nilsson, Jakob (2022). T-cell recovery and evidence of persistent immune activation 12 months after severe COVID-19. Allergy, 77(8):2468-2481.

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