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| Wnt addiction of genetically defined cancers reversed by PORCN inhibition B Madan, Z Ke, N Harmston, SY Ho, AO Frois, J Alam, DA Jeyaraj, ... Oncogene 35 (17), 2197-2207, 2016 | 382 | 2016 |
| 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 |
| anndata: Annotated data I Virshup, S Rybakov, FJ Theis, P Angerer, FA Wolf BioRxiv, 2021.12. 16.473007, 2021 | 259 | 2021 |
| 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 |
| anndata: Access and store annotated data matrices I Virshup, S Rybakov, FJ Theis, P Angerer, FA Wolf Journal of Open Source Software 9 (101), 4371, 2024 | 136 | 2024 |
| Mural lymphatic endothelial cells regulate meningeal angiogenesis in the zebrafish NI Bower, K Koltowska, C Pichol-Thievend, I Virshup, S Paterson, ... Nature Neuroscience 20 (6), 774-783, 2017 | 123 | 2017 |
| 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 |
| The impact of APP on Alzheimer-like pathogenesis and gene expression in down syndrome iPSC-derived neurons DA Ovchinnikov, O Korn, I Virshup, CA Wells, EJ Wolvetang Stem cell reports 11 (1), 32-42, 2018 | 89 | 2018 |
| Human CD141+ Dendritic Cell and CD1c+ Dendritic Cell Undergo Concordant Early Genetic Programming after Activation in Humanized Mice In Vivo Y Minoda, I Virshup, I Leal Rojas, O Haigh, Y Wong, JJ Miles, CA Wells, ... Frontiers in immunology 8, 1419, 2017 | 59 | 2017 |
| Alexander Wolf I Virshup, S Rybakov, FJ Theis, P Angerer F. anndata: Annotated data. bioRxiv 16, 2021, 2021 | 37 | 2021 |
| An open-source framework for end-to-end analysis of electronic health record data L Heumos, P Ehmele, T Treis, J Upmeier zu Belzen, E Roellin, L May, ... Nature medicine 30 (11), 3369-3380, 2024 | 32 | 2024 |
| numba/numba: Version 0.56. 4 SK Lam, A Pitrou, M Florisson, S Seibert, G Markall, TA Anderson, ... Zenodo, 2023 | 14 | 2023 |
| MAMS: matrix and analysis metadata standards to facilitate harmonization and reproducibility of single-cell data I Sarfraz, Y Wang, A Shastry, WK Teh, A Sokolov, BR Herb, HH Creasy, ... Genome Biology 25 (1), 205, 2024 | 6 | 2024 |
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| Exploratory electronic health record analysis with ehrapy L Heumos, P Ehmele, T Treis, J Upmeier zu Belzen, A Namsaraeva, ... medRxiv, 2023.12. 11.23299816, 2023 | 4 | 2023 |
| Matrix and analysis metadata standards (MAMS) to facilitate harmonization and reproducibility of single-cell data Y Wang, I Sarfraz, WK Teh, A Sokolov, BR Herb, HH Creasy, I Virshup, ... bioRxiv, 2023 | 4 | 2023 |
| chanzuckerberg/cellxgene: Release 0.15. 0 C Megill, B Martin, C Weaver, S Bell, S Badajoz, M Weiden, J Kiggins, ... Zenodo, 2020 | 3 | 2020 |
| anndataR improves interoperability between R and Python in single-cell transcriptomics L Deconinck, L Zappia, R Cannoodt, M Morgan, scverse core, I Virshup, ... bioRxiv, 2025.08. 18.669052, 2025 | 2 | 2025 |
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