Impact Publications

Feasibility of multiomics tumor profiling for guiding treatment of melanoma
Miglino, N., Toussaint, N.C., Ring, A. et al. Feasibility of multiomics tumor profiling for guiding treatment of melanoma. Nat Med 31, 2430–2441 (2025). https://doi.org/10.1038/s41591-025-03715-6

De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data
Dondi A, Borgsmüller N, Ferreira PF, et al. De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data. Genome Res. 2025;35(4):900-913. Published 2025 Apr 14. doi:10.1101/gr.279281.124

Standardization of Suspension and Imaging Mass Cytometry Single-Cell Readouts for Clinical Decision Making
Casanova R, Xu S, Bost P, et al. Standardization of suspension and imaging mass cytometry single-cell readouts for clinical decision making. Cytometry A. 2025;107(6):390-403. doi:10.1002/cyto.a.24940

Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia
Wegmann, R., Bonilla, X., Casanova, R. et al. Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia. Nat Commun 15, 9402 (2024). https://doi.org/10.1038/s41467-024-53535-4

Monitoring melanoma patients on treatments reveals a distinct macrophage population driving targeted therapy resistance
Jelena Vasilevska, Phil Fang Cheng, Julia Lehmann, Egle Ramelyte, Julia Martínez Gómez, Florentia Dimitriou, Federica Sella, Daria Ferretti, Adrian Salas-Bastos, Whitney Shannon Jordaan, Mitchell Paul Levesque, Reinhard Dummer, Lukas Sommer. Cell Reports Medicine, Volume 5, Issue 7 (2024). https://doi.org/10.1016/j.xcrm.2024.101611.

Probabilistic pathway-based multimodal factor analysis
Alexander Immer, Stefan G Stark, Francis Jacob, Ximena Bonilla, Tinu Thomas, André Kahles, Sandra Goetze, Emanuela S Milani, Bernd Wollscheid, The Tumor Profiler Consortium , Gunnar Rätsch, Kjong-Van Lehmann, Probabilistic pathway-based multimodal factor analysis, Bioinformatics, Volume 40, Issue Supplement_1, July 2024, Pages i189–i198, https://doi.org/10.1093/bioinformatics/btae216

Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer.
Dondi A, Lischetti U, Jacob F, Singer F, Borgsmüller N, Coelho R; Tumor Profiler Consortium; Heinzelmann-Schwarz V, Beisel C, Beerenwinkel N.

Learning single-cell perturbation responses using neural optimal transport.
Bunne C, Stark SG, Gut G, Del Castillo JS, Levesque M, Lehmann KV, Pelkmans L, Krause A, Rätsch G. Nat Methods. 2023 Nov;20(11):1759-1768. doi: 10.1038/s41592-023-01969-x. Epub 2023 Sep 28.

ROS Induction Targets Persister Cancer Cells with Low Metabolic Activity in NRAS-Mutated Melanoma.
Eichhoff OM, Stoffel CI, Käsler J, Briker L, Turko P, Karsai G, Zila N, Paulitschke V, Cheng PF, Leitner A, Bileck A, Zamboni N, Irmisch A, Balazs Z, Tastanova A, Pascoal S, Johansen P, Wegmann R, Mena J, Othman A, Viswanathan VS, Wenzina J, Aloia A, Saltari A, Dzung A; TuPro Consortium; Krauthammer M, Schreiber SL, Hornemann T, Distel M, Snijder B, Dummer R, Levesque MP. Cancer R (2023). doi: 10.1158/0008-5472.CAN-22-1826

scROSHI: robust supervised hierarchical identification of single cells. Prummer M, Bertolini A, Bosshard L, Barkmann F, Yates J, Boeva V; Tumor Profiler Consortium; Stekhoven D, Singer F. NAR Genom Bioinform. 2023 Jun 16;5(2):lqad058. doi: 10.1093/nargab/lqad058. eCollection 2023

scAmpi-A versatile pipeline for single-cell RNA-seq analysis from basics to clinics.
Bertolini A, Prummer M, Tuncel MA, Menzel U, Rosano-González ML, Kuipers J, Stekhoven DJ; Tumor Profiler consortium; Beerenwinkel N, Singer F. PLoS Comput Biol. (2022). doi: 10.1371/journal.pcbi.1010097

Establishing standardized immune phenotyping of metastatic melanoma by digital pathology,
Sobottka B, Nowak M, Frei AL, Haberecker M, Merki S, Tumor Profiler Consortium, Levesque MP, Dummer R, Moch H, Koelzer VH (2021),
Laboratory Investigation doi.org/10.1038/s41374-021-00653-y

The Tumor Profiler Study: Integrated, multi-​omic, functional tumor profiling for clinical decision support,
Irmisch A, Bonilla X, Chevrier S, Lehmann KV, Singer F, Toussaint NC, Esposito C, Mena J, Milani ES, Casanova R, Stekhoven DJ, Wegmann R, Jacob F, Sobottka B, Goetze S, Kuipers J, del Castillo JS, Prummer P, Tuncel M, Menzel U, Jacobs A, Engler S, Sivapatham S, Frei A, Holtackers R, Gut G, Ficek J, Dummer R, Tumor Profiler Consortium, Aebersold R, Bacac M, Beerenwinkel N, Beisel C, Bodenmiller B, Koelzer VH, Moch H, Pelkmans L, Snijder B, Tolnay M, Wollscheid B, Raetsch G, Levesque MP (2021),
Cancer Cell doi:10.1016/j.ccell.2021.01.004

SCIM: universal single-cell matching with unpaired feature sets,
Stark SG, Ficek J, Locatello F, Bonilla X, Chevrier S, Singer F, Tumor Profiler Consortium, Rätsch G, Lehmann K (2020),
Bioinformatics doi:10.1093/bioinformatics/btaa843

CATALYST: An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data,
Crowell HL, Chevrier S, Jacobs A, Sivapatham S, Tumor Profiler Consortium, Bodenmiller B, Robinson MD (2020),
F1000Research doi:10.12688/f1000research.26073.1