Analysis of functional tissue motifs for precision medicine in metastatic breast cancer

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Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

High-Dimensional T Helper Cell Profiling Reveals a Broad Diversity of Stably Committed Effector States Uncovers Interlineage Relationships

Author(s): Luigi Tortola, Andrea Jacobs, Lea Pohlmeier, Franz-Josef Obermair, Franziska Ampenberger, Bernd Bodenmiller, Manfred Kopf.
Published in: Immunity, 2020, ISSN 2666-3791
Publisher: Elsevier
DOI: 10.1016/j.immuni.2020.07.001

Clonal fitness inferred from time-series modelling of single-cell cancer genomes

Author(s): Sohrab Salehi, Farhia Kabeer, Nicholas Ceglia, Mirela Andronescu, Marc J. Williams, Kieran R. Campbell, Themina Masud, Beixi Wang, Justina Biele, Jazmine Brimhall, David Gee, Hakwoo Lee, Jerome Ting, Allen W. Zhang, Hoa Tran, Ciara O'Flanagan, Fatemeh Dorri, Nicole Rusk, Teresa de Algara, So Ra Lee, Brian Y.C. Cheng, Peter Eirew, Takako Kono, Jenifer Pham, Diljot Grewal, Daniel Lai, Richard Moore,
Published in: Nature, 2021, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-021-03648-3

Standardization of Suspension and Imaging Mass Cytometry Single‐Cell Readouts for Clinical Decision Making

Author(s): Ruben Casanova, Shuhan Xu, Pierre Bost, Sujana Sivapatham, Andrea Jacobs, Stefanie Engler, null null, Mitchell P. Levesque, Reinhard Dummer, Bernd Bodenmiller, Stéphane Chevrier
Published in: Cytometry Part A, Issue 107, 2025, Page(s) 390-403, ISSN 1552-4922
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cyto.a.24940

Cell-to-cell and type-to-type heterogeneity of signaling networks: insights from the crowd

Author(s): Attila Gabor, Marco Tognetti, Alice Driessen, Jovan Tanevski, Baosen Guo, Wencai Cao, He Shen, Thomas Yu Verena Chung, Single Cell Signaling in Breast Cancer DREAM Consortium members, Bernd Bodenmiller1, Julio Saez-Rodriguez1
Published in: Molecular Systems Biology, Issue 2021 Oct;17(10), 2021, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.202110402

Multiplex protein imaging in tumour biology

Author(s): Natalie de Souza, Shan Zhao, Bernd Bodenmiller
Published in: Nature Reviews Cancer, Issue 24, 2024, Page(s) 171-191, ISSN 1474-175X
Publisher: Nature Publishing Group
DOI: 10.1038/s41568-023-00657-4

Mass cytometric and transcriptomic profiling of epithelial-mesenchymal transitions in human mammary cell lines.

Author(s): Johanna Wagner, Markus, Masek, Andrea Jacobs, Charlotte Soneson, Sujana Sivapatham, Nicolas Damond, Natalie de Souza, Mark D. Robinson, Bernd Bodenmiller.
Published in: Scientific Data, Issue 2022 Apr;7(70), 2022, ISSN 2052-4463
Publisher: Nature Publishing Group
DOI: 10.1038/s41597-022-01137-4

Establishing standardized immune phenotyping of metastatic melanoma by digital pathology.

Author(s): Bettina Sobottka, Marta Nowak, Anja L. Frei, Martina Haberecker, Samuel Merki, Tumor Profiler consortium, Mitchell P. Levesque, Reinhard Dummer, Holger Moch, Viktor H. Koelzer.
Published in: Laboratory Investigation, Issue 2021 Dec;101(12, 2021, ISSN 0023-6837
Publisher: Nature Publishing Group
DOI: 10.1038/s41374-021-00653-y

A stratification system for breast cancer based on basoluminal tumor cells and spatial tumor architecture

Author(s): Lasse Meyer, Hartland W. Jackson, Nils Eling, Shan Zhao, Genki Usui, Haithem Dakhli, Peter Schraml, Susanne Dettwiler, Constanze Elfgen, Zsuzsanna Varga, Holger Moch, Natalie de Souza, Bernd Bodenmiller
Published in: Cancer Cell, Issue 43, 2025, Page(s) 1637-1655.e9, ISSN 1535-6108
Publisher: Cell Press
DOI: 10.1016/j.ccell.2025.06.019

A comprehensive single-cell map of T cell exhaustion-associated immune environments in human breast cancer

Author(s): Sandra Tietscher, Johanna Wagner, Tobias Anzeneder, Claus Langwieder, Martin Rees, Bettina Sobottka, Natalie de Souza, Bernd Bodenmiller
Published in: Nature Communications, Issue 14, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-35238-w

Cancer Research in the Age of Spatial Omics: Lessons from IMAXT

Author(s): Dario Bressan, null null, Nicholas Walton, Gregory J. Hannon, null null, Mohammad Al Sa’d, Bruno Albuquerque, Hamid Raza Ali, Martina Alini, Samuel Aparicio, Heather Ashmore, Thomas Ashmore, Vinci Au, Shankar Balasubramanian, Caroline Baril, Giorgia Battistoni, Sean Beatty, Robby Becker, Bernd Bodenmiller, Alina Bollhagen, Carla Boquetale, Edward S. Boyden, Dario Bressan, Alejandra Bruna, Marcel
Published in: Cancer Discovery, Issue 15, 2025, Page(s) 16-21, ISSN 2159-8274
Publisher: American Association for Cancer Research Inc.
DOI: 10.1158/2159-8290.cd-24-1686

Landscapes of cellular phenotypic diversity in breast cancer xenografts and their impact on drug response

Author(s): Dimitra Georgopoulou, Maurizio Callari, Oscar M. Rueda, Abigail Shea,. Alistair Martin, Agnese Giovannetti, Fatime Qosaj, Ali Dariush, Suet-Feung Chin, Larissa S. Carnevalli, Elena Provenzano, Wendy Greenwood, Giulia Lerda, Elham Esmaeilishirazifard, Martin O'Reilly, Violeta Serra, Dario Bressan, IMAXT Consortium, Gordon B. Mills, H. Raza Ali, Sabina S Cosulich, Gregory J. Hannon, Alejandra Bruna,
Published in: Nature Communications, Issue Mar 31;12(1), 2021, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-22303-z

Profound dysregulation of T cell homeostasisand function in patients with severe COVID-19.

Author(s): Sarah Adamo, Stéphane Chevrier, Carlo Cervia, Yves Zurbuchen, Miro E. Raeber, Lilinae Yang, Sujana Sivapatham, Andrea Jacobs, Esther Baechli, Alain Rudiger, Melina Stüssi-Helbling, Lars C. Huber, Dominik J. Schaer, Bernd Bodenmiller1, Onur Boyman1, Jakob Nilsson1.
Published in: Allergy, Issue Apr 21, 2021, ISSN 0105-4538
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/all.14866

LifeTime improving European healthcare through cell-based interceptive medicine

Author(s): Nikolaus Rajewsky, Geneviève Almouzni, Stanislaw A. Gorski, Stein Aerts, Ido Amit, Michela G. Bertero, Christoph Bock, Annelien L. Bredenoord, Giacomo Cavall, Susanne Chiocca, Hans Clevers, Bart De Strooper, Angelika Eggert, Jan Ellenberg, Xosé M. Fernández, Marek Figlerowicz, Susan M. Gasser, Norbert Hubner, Jorgen Kjems, Jürgen A. Knoblich, Grietje Krabbe, Peter Lichter, Sten Linnarsson, Jea
Published in: Nature, 2020, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-020-2715-9

Cytomapper: an R/bioconductor package for visualisation of highly multiplexed imaging data

Author(s): Nils Eling, Nicolas Damond, Tobias Hoch, Bernd Bodenmiller
Published in: Bioinformatics, 2020, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa1061

Monogenic Diabetes and Integrated Stress Response Genes Display Altered Gene Expression in Type 1 Diabetes.

Author(s): Helmut Hiller, Dawn E. Beachy, Jospeh J. Lebowitz, Stefanie Engler, Justin R. Mason, Douglas R. Miller, Irina Kusmarteva, Laura M. Jacobsen, Amanda L. Posgai, Habibeh Khoshbouei, Richard A. Oram, Desmond A. Schatz, Andrew T. Hattersley, Bernd Bodenmiller, Mark A. Atkinson, Harry S. Nick, Clive H. Wasserfall
Published in: Diabetes, Issue 2021 Aug;70(8), 2021, ISSN 0012-1797
Publisher: American Diabetes Association
DOI: 10.2337/db21-0070

Statistical modeling and analysis of cell counts from multiplexed imaging data

Author(s): Pierre Bost, Ruben Casanova, Uria Mor, Martina Haberecker, Chantal Pauli, Susanne Dettwiler, Bernd Bodenmiller
Published in: Cell Systems, Issue 16, 2025, Page(s) 101296, ISSN 2405-4712
Publisher: Elsevier BV
DOI: 10.1016/j.cels.2025.101296

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems

Author(s): Shahar Alon, Daniel R. Goodwin, Anubhav Sinha, Asmamaw T. Wassie, Fei Chen, Evan R. Daugharthy, Yosuke Bando, Atsushi Kajita, Andrew Xue, Karl Marrett, Robert Prior, Yi Cui, Andrew C. Payne, Chun-Chen Yao, Ho-Jun Suk, Ru Wang, Chih-Chieh Jay Yu, Paul Tillberg, Paul Reginato, Nikita Pak, Songlei Liu, Sukanya Punthambaker, Eswar P.R. Iyer, Richie E. Kohman, Jeremy A. Miller, Ed S. Lein, Ana Lako, Ni
Published in: Science, 2021, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aax2656

A quantitative analysis of the interplay of environment, neighborhood, cell state in 3D spheroids

Author(s): Vito R.T. Zanotelli, Matthias Leutenegger, Xiao-Kang Lun, Fanny Georgi, Natalie de Souza, Bernd Bodenmiller
Published in: Molecular Systems Biology, 2020, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.20209798

Precision Oncology Program (POP), an observational study using real-world data and imaging mass cytometry to explore decision support for the Molecular Tumor Board: study protocol

Author(s): Laura Amanda Boos, Christian Doerig, Gabriele Gut, Nicola Miglino, Luis Fábregas Ibáñez, Shemra Rizzo, Charlotta Schärfe Fruechtenicht, Nandini Chitale, Charles Lu, Martin Zoche, Bernd Bodenmiller, Stephane Chevrier, Alexandra Sophia Eklund, Marta Nowak, Sepehr Rahmani Khajouei, Carmen Galani Berardo, Lukasz Kaczmarek, Karin Bosshard, William Archey, Matthias Bodmer, Dominik Glinz, Eva Camaril
Published in: BMJ Open, Issue 15, 2025, Page(s) e096591, ISSN 2044-6055
Publisher: BMJ Publishing Group
DOI: 10.1136/bmjopen-2024-096591

Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment

Author(s): Laura Kuett, Raul Catena, Alaz Özcan, Alex Plüss A, Cancer Grand Challenges IMAXT Consortium, Peter Schraml, Holger Moch, Natalie de Souza, Bernd Bodenmiller.
Published in: Nature Cancer, Issue 2022 Jan;3(1):, 2022, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s43018-021-00301-w

cytoviewer: an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data

Author(s): Lasse Meyer, Nils Eling, Bernd Bodenmiller
Published in: BMC Bioinformatics, Issue 25, 2024, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-023-05546-z

Sensitive detection of minimal residual disease and immunotherapy targets by multi-modal bone marrow analysis in high-risk neuroblastoma – a multi-center study

Author(s): Nina U. Gelineau, Eva Bozsaky, Lieke M. J. van Zogchel, Fikret Rifatbegovic, Daria Lazic, Andrea Ziegler, Ahmad Javadi, Lily Zappeij-Kannegieter, Ulrike Pötschger, Marta Fiocco, Peter F. Ambros, Inge M. Ambros, Bernd Bodenmiller, Ellen C. van der Schoot, Ruth Ladenstein, Marie Bernkopf, Godelieve A. M. Tytgat, Sabine Taschner-Mandl
Published in: Journal of Experimental & Clinical Cancer Research, Issue 44, 2025, ISSN 1756-9966
Publisher: Springer Science and Business Media LLC
DOI: 10.1186/s13046-025-03481-w

Distant Metastases of Breast Cancer Resemble Primary Tumors in Cancer Cell Composition but Differ in Immune Cell Phenotypes

Author(s): Laura Kuett, Alina Bollhagen, Sandra Tietscher, Bettina Sobottka, Nils Eling, Zsuzsanna Varga, Holger Moch, Natalie de Souza, Bernd Bodenmiller
Published in: Cancer Research, Issue 85, 2025, Page(s) 15-31, ISSN 0008-5472
Publisher: American Association for Cancer Research
DOI: 10.1158/0008-5472.can-24-1211

Multi-omics reveals clinically relevant proliferative drive associated with mTOR-MYC-OXPHOS activity in chronic lymphocytic leukemia.

Author(s): Junyan Lu, Ester Cannizzaro, Fabienne Meier-Abt, Sebastian Scheinost, Peter-Martin Bruch, Holly A. Giles, Almut Lütge, Jennifer Hüllein, Lena Wagner, Brian Giacopelli, Ferran Nadeu, Julio Delgado, Elias Campo, Maurizio Mangolini, Ingo Ringshausen, Martin Böttcher, Dimitros Mougiakakos, Andrea Jacobs, Bernd Bodenmiller, Sascha Dietrich, Christopher C. Oakes, Thorsten Zenz, Wolfgang Huber.
Published in: Nature Cancer, Issue 2021 Aug;2(8), 2021, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s43018-021-00216-6

SCIM: universal single-cell matching with unpaired feature sets

Author(s): Stefan G. Stark, Joanna Ficek, Francesco Locatello, Ximena Bonilla, Stéphane Chevrier, Franziska Singer, Tumor Profiler Consortium, Gunnar Rätsch, Kjong-Van Lehmann
Published in: Bioinformatics, 2020, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa843

Cutaneous and systemic hyperinflammation drives maculopapular drug exanthema in severely ill COVID-19 patients.

Author(s): Ysutaka Mitamura, Daniel Schulz, Saskia Oro, Nick Li, Isabel Kolm, Claudia Lang, Reihane Ziadlou, Ge Tan, Bernd Bodenmiller, Peter Steiger, Angelo Marzano, Nicolas de Prost, Olivier Caudin, Mitchell Levesque, Corinne Stoffel, Peter Schmid-Grendelmeier, Emanual Maverakis, Cezim A. Akdis, Marie-Charlotte Brüggen.
Published in: Allergy, Issue 2021 Jun 22, 2021, ISSN 0105-4538
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/all.14983

Feasibility of multiomics tumor profiling for guiding treatment of melanoma

Author(s): Nicola Miglino, Nora C. Toussaint, Alexander Ring, Ximena Bonilla, Marina Tusup, Benedict Gosztonyi, Tarun Mehra, Gabriele Gut, Francis Jacob, Stephane Chevrier, Kjong-Van Lehmann, Ruben Casanova, Andrea Jacobs, Sujana Sivapatham, Laura Boos, Parisa Rahimzadeh, Manuel Schuerch, Bettina Sobottka, Natalia Chicherova, Shuqing Yu, Rebekka Wegmann, Julien Mena, Emanuela S. Milani, Sandra Goetze, Cinzia
Published in: Nature Medicine, Issue 31, 2025, Page(s) 2430-2441, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-025-03715-6

An end-to-end workflow for multiplexed image processing and analysis

Author(s): Jonas Windhager, Vito Riccardo Tomaso Zanotelli, Daniel Schulz, Lasse Meyer, Michelle Daniel, Bernd Bodenmiller, Nils Eling
Published in: Nature Protocols, Issue 18, 2023, Page(s) 3565-3613, ISSN 1754-2189
Publisher: Nature Publishing Group
DOI: 10.1038/s41596-023-00881-0

Breast tumor microenvironment structures are associated with genomic features and clinical outcome.

Author(s): Esther Danenberg, Helen Bardwell, Vito R.T.Zanotelli, Elena Provenzano, Suet-Fueng Chin, Oscar M. Rueda Andrew Green, Emad Rakha, Samuel Aparicio, Ian O. Ellis, Bernd Bodenmiller1, Carlos Caldas1, H. Raza Ali1.
Published in: Nature Genetics, Issue 2022 Apr 18, 2022, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-022-01041-y

Multielement Z-tag imaging by X-ray fluorescence microscopy for next-generation multiplex imaging

Author(s): Merrick Strotton, Tsuyoshi Hosogane, Marco di Michiel, Holger Moch, Zsuzsanna Varga, Bernd Bodenmiller
Published in: Nature Methods, Issue 20, 2023, Page(s) 1310-1322, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-023-01977-x

Classifying cancer-associated fibroblasts—The good, the bad, and the target

Author(s): Lena Cords, Natalie de Souza, Bernd Bodenmiller
Published in: Cancer Cell, Issue 42, 2025, Page(s) 1480-1485, ISSN 1535-6108
Publisher: Cell Press
DOI: 10.1016/j.ccell.2024.08.011

Mechanistic Model of Signaling Dynamics Across an Epithelial Mesenchymal Transition.

Author(s): James D. Wade, Xiao-Kang Lun, Nevena Zivanovic, Eberhard O. Voit1, Bernd Bodenmiller1
Published in: Frontiers in Physiology, 2020, ISSN 1664-042x
Publisher: Frontiers Research Foundation
DOI: 10.3389/fphys.2020.579117

A distinct innate immune signature marks progression from mild to severe COVID-19

Author(s): Stéphane Chevrier, Yves Zurbuchen, Carlo Cervia, Sarah Adamo, Miro E. Raeber, Natalie de Souza, Sujana Sivapatham, Andrea Jacobs, Esther Bachli, Alain Rudiger, Melina Stüssi-Helbling, Lars C. Huber, Dominik J. Schaer, Jakob Nilsson1, Onur Boyman1, Bernd Bodenmiller1.
Published in: Cell Reports Medicine, 2020, ISSN 2666-3791
Publisher: Cell Press (Elsevier)
DOI: 10.1016/j.xcrm.2020.100166

Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy.

Author(s): Tobias Hoch, Daniel Schulz, Nils Eling, Julia Martínez Gómez, Mitchell P. Levesque, Bernd Bodenmiller
Published in: Science Immunology, Issue 2022 Apr;7(70, 2022, ISSN 2470-9468
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciimmunol.abk1692

DNA-barcoded signal amplification for imaging mass cytometry enables sensitive and highly multiplexed tissue imaging

Author(s): Tsuyoshi Hosogane, Ruben Casanova, Bernd Bodenmiller
Published in: Nature Methods, Issue 20, 2023, Page(s) 1304-1309, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-023-01976-y

Compressed sensing expands the multiplexity of imaging mass cytometry

Author(s): Tsuyoshi Hosogane, Leonor Schubert Santana, Nils Eling, Holger Moch, Bernd Bodenmiller
Published in: Nature Communications, Issue 16, 2025, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-025-66629-4

Cancer-associated fibroblast classification in single-cell and spatial proteomics data

Author(s): Lena Cords, Sandra Tietscher, Tobias Anzeneder, Claus Langwieder, Martin Rees, Natalie de Souza, Bernd Bodenmiller
Published in: Nature Communications, Issue 14, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-39762-1

Integrating Formalin-Fixed, Paraffin-Embedded–Derived Whole-Genome Sequencing into Routine Molecular Pathology

Author(s): Cassandra Litchfield, Ronny Nienhold, Andreas Wicki, Michael Schmid, Domingo Aguilera-Garcia, Viktor Hendrik Koelzer, Rudolf Aebersold, Melike Ak, Faisal S. Al-Quaddoomi, Silvana I. Albert, Jonas Albinus, Ilaria Alborelli, Sonali Andani, Per-Olof Attinger, Marina Bacac, Monica-Andreea Baciu-Drăgan, Daniel Baumhoer, Beatrice Beck-Schimmer, Niko Beerenwinkel, Christian Beisel, Lara Bernasconi, Anne
Published in: The Journal of Molecular Diagnostics, Issue 27, 2025, Page(s) 722-735, ISSN 1525-1578
Publisher: American Society for Investigative Pathology
DOI: 10.1016/j.jmoldx.2025.04.011

Optimizing multiplexed imaging experimental design through tissue spatial segregation estimation

Author(s): Pierre Bost, Daniel Schulz, Stefanie Engler, Clive Wasserfall, Bernd Bodenmiller
Published in: Nature Methods, Issue 20, 2023, Page(s) 418-423, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-022-01692-z

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