| Multiplexed protein maps link subcellular organization to cellular states G Gut, MD Herrmann, L Pelkmans Science 361 (6401), eaar7042, 2018 | 449 | 2018 |
| Learning single-cell perturbation responses using neural optimal transport C Bunne, SG Stark, G Gut, JS Del Castillo, M Levesque, KV Lehmann, ... Nature Methods 20 (11), 1759-1768, 2023 | 122 | 2023 |
| The Tumor Profiler Study: Integrated, multi-omic, functional tumor profiling for clinical decision support A Irmisch, X Bonilla, S Chevrier, KV Lehmann, F Singer, NC Toussaint, ... Cancer cell 39 (3), 288-293, 2021 | 116 | 2021 |
| Trajectories of cell-cycle progression from fixed cell populations G Gut, MD Tadmor, D Pe'er, L Pelkmans, P Liberali Nature methods 12 (10), 951-954, 2015 | 114 | 2015 |
| Multimodal spatiotemporal phenotyping of human retinal organoid development P Wahle, G Brancati, C Harmel, Z He, G Gut, JS Del Castillo, ... Nature Biotechnology 41 (12), 1765-1775, 2023 | 65 | 2023 |
| SCIM: universal single-cell matching with unpaired feature sets SG Stark, J Ficek, F Locatello, X Bonilla, S Chevrier, F Singer, G Rätsch, ... Bioinformatics 36 (Supplement_2), i919-i927, 2020 | 54 | 2020 |
| An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data HL Crowell, S Chevrier, A Jacobs, S Sivapatham, B Bodenmiller, ... F1000Research 9, 1263, 2022 | 43 | 2022 |
| Establishing standardized immune phenotyping of metastatic melanoma by digital pathology B Sobottka, M Nowak, AL Frei, M Haberecker, S Merki, MP Levesque, ... Laboratory investigation 101 (12), 1561-1570, 2021 | 31 | 2021 |
| Characterization of the neurogenic niche in the aging dentate gyrus using iterative immunofluorescence imaging JD Cole, JS Del Castillo, G Gut, D Gonzalez-Bohorquez, L Pelkmans, ... Elife 11, e68000, 2022 | 27 | 2022 |
| Neural Unbalanced Optimal Transport via Cycle-Consistent Semi-Couplings F Lübeck, C Bunne, G Gut, JS del Castillo, L Pelkmans, D Alvarez-Melis arXiv preprint arXiv:2209.15621, 2022 | 20 | 2022 |
| Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer A Dondi, U Lischetti, F Jacob, F Singer, N Borgsmüller, R Coelho, ... Nature Communications 14 (1), 7780, 2023 | 18 | 2023 |
| scAmpi—A versatile pipeline for single-cell RNA-seq analysis from basics to clinics A Bertolini, M Prummer, MA Tuncel, U Menzel, ML Rosano-González, ... PLoS computational biology 18 (6), e1010097, 2022 | 15 | 2022 |
| Iterative Indirect Immunofluorescence Imaging (4i) on Adherent Cells and Tissue Sections BA Kramer, JS Del Castillo, L Pelkmans, G Gut Bio-protocol 13 (13), 2023 | 10 | 2023 |
| Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing for personalized oncology A Dondi, U Lischetti, F Jacob, F Singer, N Borgsmüller, ... bioRxiv, 2022.12. 12.520051, 2022 | 5 | 2022 |
| An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data. F1000Res. 9, 1263 HL Crowell, S Chevrier, A Jacobs, S Sivapatham, ... | 4 | 2020 |
| Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia R Wegmann, X Bonilla, R Casanova, S Chevrier, R Coelho, C Esposito, ... Nature Communications 15 (1), 9402, 2024 | 3 | 2024 |
| AI-powered virtual tissues from spatial proteomics for clinical diagnostics and biomedical discovery J Wenckstern, E Jain, K Vasilev, M Pariset, A Wicki, G Gut, C Bunne arXiv preprint arXiv:2501.06039, 2025 | 1 | 2025 |
| Monitoring melanoma patients on treatment reveals a distinct macrophage population driving targeted therapy resistance J Vasilevska, PF Cheng, J Lehmann, E Ramelyte, JM Gómez, F Dimitriou, ... Cell Reports Medicine 5 (7), 2024 | 1 | 2024 |
| HistoPlexer: Histopathology-based Protein Multiplex Generation using Deep Learning S Andani, B Chen, J Ficek-Pascual, S Heinke, R Casanova, B Hild, ... medRxiv, 2024.01. 26.24301803, 2024 | 1 | 2024 |
| Standardization of suspension and imaging mass cytometry readouts for clinical decision making R Casanova, S Xu, S Sivapatham, A Jacobs, S Engler, ... bioRxiv, 2023.03. 19.531228, 2023 | 1 | 2023 |
