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 | 438 | 2022 |
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 | 308 | 2023 |
Spatial components of molecular tissue biology G Palla, DS Fischer, A Regev, FJ Theis Nature Biotechnology 40 (3), 308-318, 2022 | 184 | 2022 |
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 | 109 | 2019 |
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 | 77 | 2023 |
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 | 41 | 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 | 33* | 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, 1-5, 2024 | 24 | 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 | 22 | 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 | 20 | 2018 |
Mapping cells through time and space with moscot D Klein, G Palla, M Lange, M Klein, Z Piran, M Gander, ... bioRxiv, 2023.05. 11.540374, 2023 | 19 | 2023 |
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 | 5 | 2022 |
Latent factor modeling of scRNA-seq data uncovers dysregulated pathways in autoimmune disease patients G Palla, E Ferrero Iscience 23 (9), 2020 | 5 | 2020 |
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, ... bioRxiv, 2024.02. 02.578605, 2024 | 2 | 2024 |
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 | 2 | 2023 |
Unbalanced low-rank optimal transport solvers M Scetbon, M Klein, G Palla, M Cuturi Advances in Neural Information Processing Systems 36, 2024 | 1 | 2024 |
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 | 1 | 2024 |
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 | 1 | 2022 |
VIB Hackathon on spatial omics tools and methods B Rombaut, L Pollaris, C Sang-aram, MV Cruysse, R Cannoodt, ... | | 2024 |
Defining and benchmarking open problems in single-cell analysis MD Luecken, S Gigante, DB Burkhardt, R Cannoodt, DC Strobl, ... Research Square, 2024 | | 2024 |