| Best practices for single-cell analysis across modalities L Heumos, AC Schaar, C Lance, A Litinetskaya, F Drost, L Zappia, ... Nature Reviews Genetics 24 (8), 550-572, 2023 | 1003 | 2023 |
| Squidpy: a scalable framework for spatial omics analysis G Palla, H Spitzer, M Klein, D Fischer, AC Schaar, LB Kuemmerle, ... Nature methods 19 (2), 171-178, 2022 | 959 | 2022 |
| Spatial components of molecular tissue biology G Palla, DS Fischer, A Regev, FJ Theis Nature Biotechnology 40 (3), 308-318, 2022 | 345 | 2022 |
| The scverse project provides a computational ecosystem for single-cell omics data analysis I Virshup, D Bredikhin, L Heumos, G Palla, G Sturm, A Gayoso, I Kats, ... Nature biotechnology 41 (5), 604-606, 2023 | 286 | 2023 |
| SpatialData: an open and universal data framework for spatial omics L Marconato, G Palla, KA Yamauchi, I Virshup, E Heidari, T Treis, ... Nature methods 22 (1), 58-62, 2025 | 161 | 2025 |
| Quantification of differential transcription factor activity and multiomics-based classification into activators and repressors: diffTF I Berest, C Arnold, A Reyes-Palomares, G Palla, KD Rasmussen, H Giles, ... Cell reports 29 (10), 3147-3159. e12, 2019 | 146 | 2019 |
| Mapping cells through time and space with moscot D Klein, G Palla, M Lange, M Klein, Z Piran, M Gander, ... Nature 638 (8052), 1065-1075, 2025 | 127 | 2025 |
| OME-Zarr: a cloud-optimized bioimaging file format with international community support J Moore, D Basurto-Lozada, S Besson, J Bogovic, J Bragantini, EM Brown, ... Histochemistry and Cell Biology 160 (3), 223-251, 2023 | 121 | 2023 |
| GRaNIE and GRaNPA: inference and evaluation of enhancer‐mediated gene regulatory networks A Kamal, C Arnold, A Claringbould, R Moussa, NH Servaas, M Kholmatov, ... Molecular Systems Biology 19 (6), e11627, 2023 | 71* | 2023 |
| Nicheformer: a foundation model for single-cell and spatial omics AC Schaar, A Tejada-Lapuerta, G Palla, R Gutgesell, L Halle, M Minaeva, ... bioRxiv, 2024.04. 15.589472, 2024 | 67 | 2024 |
| Multimodal characterization of murine gastruloid development S Suppinger, M Zinner, N Aizarani, I Lukonin, R Ortiz, C Azzi, MB Stadler, ... Cell Stem Cell 30 (6), 867-884. e11, 2023 | 67 | 2023 |
| Defining and benchmarking open problems in single-cell analysis MD Luecken, S Gigante, DB Burkhardt, R Cannoodt, DC Strobl, ... Nature Biotechnology, 1-6, 2025 | 39 | 2025 |
| Unbalancedness in neural monge maps improves unpaired domain translation L Eyring, D Klein, T Uscidda, G Palla, N Kilbertus, Z Akata, F Theis arXiv preprint arXiv:2311.15100, 2023 | 29 | 2023 |
| Increased B-cell activating factor (BAFF)/B-lymphocyte stimulator (BLyS) in primary antiphospholipid syndrome is associated with higher adjusted global antiphospholipid … LL van den Hoogen, G Palla, CPJ Bekker, RDE Fritsch-Stork, ... RMD open 4 (2), e000693, 2018 | 25 | 2018 |
| Nicheformer: a foundation model for single-cell and spatial omics A Tejada-Lapuerta, AC Schaar, R Gutgesell, G Palla, L Halle, M Minaeva, ... Nature methods, 1-14, 2025 | 17 | 2025 |
| GraphCompass: spatial metrics for differential analyses of cell organization across conditions M Ali, M Kuijs, S Hediyeh-Zadeh, T Treis, K Hrovatin, G Palla, AC Schaar, ... Bioinformatics 40 (Supplement_1), i548-i557, 2024 | 16 | 2024 |
| Modeling single-cell dynamics using unbalanced parameterized Monge maps LV Eyring, D Klein, G Palla, S Becker, P Weiler, N Kilbertus, FJ Theis bioRxiv, 2022.10. 04.510766, 2022 | 14 | 2022 |
| A Cross-Species Generative Cell Atlas Across 1.5 Billion Years of Evolution: The TranscriptFormer Single-cell Model JD Pearce, SE Simmonds, G Mahmoudabadi, L Krishnan, G Palla, ... bioRxiv, 2025.04. 25.650731, 2025 | 12 | 2025 |
| Unbalanced low-rank optimal transport solvers M Scetbon, M Klein, G Palla, M Cuturi Advances in Neural Information Processing Systems 36, 52312-52325, 2023 | 10 | 2023 |
| Uncertainty quantification for atlas-level cell type transfer J Engelmann, L Hetzel, G Palla, L Sikkema, M Luecken, F Theis arXiv preprint arXiv:2211.03793, 2022 | 7 | 2022 |
