SCIM: universal single-cell matching with unpaired feature sets. - Stefan G. Stark; Joanna Ficek; Francesco Locatello; Ximena Bonilla; Stéphane Chevrier; Franziska Singer; Tumor Profiler Consortium; Gunnar Rätsch; Kjong-Van Lehmann (Bioinform., 2020)

An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data. - Helena L. Crowell; Stéphane Chevrier; Andrea Jacobs; Sujana Sivapatham; Tumor Profiler Consortium; Bernd Bodenmiller; Mark D. Robinson (F1000Research, 2020)

scAmpi - A versatile pipeline for single-cell RNA-seq analysis from basics to clinics. - Anne Bertolini; Michael Prummer; Mustafa Anil Tuncel; Ulrike Menzel; María Lourdes Rosano-González; Jack Kuipers; Daniel J. Stekhoven; Tumor Profiler Consortium; Niko Beerenwinkel; Franziska Singer (PLoS Comput. Biol., 2022)

Probabilistic pathway-based multimodal factor analysis. - Alexander Immer; Stefan G. Stark; Francis Jacob; Ximena Bonilla; Tinu Thomas; André Kahles; Sandra Götze; Emanuela S. Milani; Bernd Wollscheid; Tumor Profiler Consortium; Gunnar Rätsch; Kjong-Van Lehmann (Bioinform., 2024)

Towards AI-Based Precision Oncology: A Machine Learning Framework for Personalized Counterfactual Treatment Suggestions based on Multi-Omics Data. - Manuel Schürch; Laura Boos; Viola Heinzelmann-Schwarz; Gabriele Gut; Michael Krauthammer; Andreas Wicki; Tumor Profiler Consortium (CoRR, 2024)