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Impact Publications


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. Nat Commun. 2023 Nov 27;14(1):7780. doi: 10.1038/s41467-023-43387-9.

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

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

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