| 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 | 212 | 2023 |
| An integrated cell atlas of the lung in health and disease L Sikkema, C Ramírez-Suástegui, DC Strobl, TE Gillett, L Zappia, ... Nature Medicine 29 (6), 1563-1577, 2023 | 192* | 2023 |
| Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis A Bastidas-Ponce, S Tritschler, L Dony, K Scheibner, M Tarquis-Medina, ... Development 146 (12), dev173849, 2019 | 177 | 2019 |
| Cell-type-specific impact of glucocorticoid receptor activation on the developing brain: a cerebral organoid study C Cruceanu, L Dony, AC Krontira, DS Fischer, S Roeh, R Di Giaimo, ... American Journal of Psychiatry 179 (5), 375-387, 2022 | 50* | 2022 |
| Sfaira accelerates data and model reuse in single cell genomics DS Fischer, L Dony, M König, A Moeed, L Zappia, L Heumos, S Tritschler, ... Genome Biology 22, 1-21, 2021 | 27 | 2021 |
| Parametric and non-parametric gradient matching for network inference: a comparison L Dony, F He, MPH Stumpf BMC bioinformatics 20, 1-12, 2019 | 7* | 2019 |
| Out-of-distribution prediction with disentangled representations for single-cell RNA sequencing data M Lotfollahi, L Dony, H Agarwala, F Theis bioRxiv, 2021.09. 01.458535, 2021 | 6 | 2021 |
| Variational autoencoders with flexible priors enable robust distribution learning on single-cell RNA sequencing data L Dony, M König, D Fischer, FJ Theis ICML 2020 Workshop on Computational Biology (WCB) Proceedings Paper 37, 2020 | 5 | 2020 |
| An integrated transcriptomic cell atlas of human neural organoids Z He, L Dony, JS Fleck, A Szalata, KX Li, I Sliskovic, HC Lin, M Santel, ... bioRxiv, 2023.10. 05.561097, 2023 | 4 | 2023 |
| Human cortical neurogenesis is altered via glucocorticoid-mediated regulation of ZBTB16 expression AC Krontira, C Cruceanu, L Dony, C Kyrousi, MH Link, N Rek, D Pöhlchen, ... Neuron, 2024 | 2 | 2024 |
| Data-driven dynamical modelling of a pathogen-infected plant gene regulatory network: A comparative analysis M Foo, L Dony, F He Biosystems 219, 104732, 2022 | 1 | 2022 |
| PEITH (Θ): perfecting experiments with information theory in Python with GPU support L Dony, J Mackerodt, S Ward, S Filippi, MPH Stumpf, J Liepe Bioinformatics 34 (7), 1249-1250, 2018 | 1 | 2018 |
| 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 | | 2024 |
| Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids L Dony, AC Krontira, L Kaspar, R Ahmad, IS Demirel, M Grochowicz, ... bioRxiv, 2024.01. 21.576532, 2024 | | 2024 |
| Effects of glucocorticoid exposure on gene expression and cell fate specification in cerebral organoids L Kaspar, L Dony, C Cruceanu, EB Binder, FJ Theis Neuroscience Applied 2, 101038, 2023 | | 2023 |
| Brain organoids as models of the developing human brain: deciphering the molecular signature of prenatal stress C Cruceanu, L Dony, AC Kontira, D Fischer, S Roeh, R Di Giaimo, ... European Neuropsychopharmacology 29, S7-S8, 2019 | | 2019 |
