2022
- Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing for personalized oncology, Dondi A, Lischetti U, Jacob F, Singer F, Borgsmüller N, Tumor Profiler Consortium, Heinzelmann-Schwarz V, Christian Beisel C, Niko Beerenwinkel N (2022), under review
2021
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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
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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 (2021), bioRxiv doi:10.1101/2021.03.25.437054
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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
2020
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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
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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