| Squidpy: a scalable framework for spatial omics analysis G Palla, H Spitzer, M Klein, D Fischer, AC Schaar, LB Kuemmerle, ... Nature Methods, 1-8, 2022 | 956 | 2022 |
| Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics C Muus, MD Luecken, G Eraslan, L Sikkema, A Waghray, G Heimberg, ... Nature medicine 27 (3), 546-559, 2021 | 669* | 2021 |
| Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation AD Brunner, M Thielert, C Vasilopoulou, C Ammar, F Coscia, A Mund, ... Molecular Systems Biology 18 (3), e10798, 2022 | 564 | 2022 |
| Spatial components of molecular tissue biology G Palla, DS Fischer, A Regev, FJ Theis Nature Biotechnology 40 (3), 308-318, 2022 | 342 | 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 |
| Single cells make big data: new challenges and opportunities in transcriptomics P Angerer, L Simon, S Tritschler, FA Wolf, D Fischer, FJ Theis Current Opinion in Systems Biology 4, 85-91, 2017 | 265 | 2017 |
| Concepts and limitations for learning developmental trajectories from single cell genomics S Tritschler, M Büttner, DS Fischer, M Lange, V Bergen, H Lickert, ... Development 146 (12), 2019 | 236 | 2019 |
| Modeling intercellular communication in tissues using spatial graphs of cells DS Fischer, AC Schaar, FJ Theis Nature Biotechnology, 1-5, 2022 | 226* | 2022 |
| Impulse model-based differential expression analysis of time course sequencing data DS Fischer, FJ Theis, N Yosef Nucleic acids research 46 (20), e119-e119, 2018 | 148 | 2018 |
| Inferring population dynamics from single-cell RNA-sequencing time series data DS Fischer, AK Fiedler, EM Kernfeld, RMJ Genga, A Bastidas-Ponce, ... Nature biotechnology 37 (4), 461-468, 2019 | 144 | 2019 |
| Predicting antigen specificity of single T cells based on TCR CDR 3 regions DS Fischer, Y Wu, B Schubert, FJ Theis Molecular systems biology 16 (8), e9416, 2020 | 134 | 2020 |
| EpiScanpy: integrated single-cell epigenomic analysis A Danese, ML Richter, K Chaichoompu, DS Fischer, FJ Theis, ... Nature Communications 12 (1), 1-8, 2021 | 132 | 2021 |
| MPRAnalyze: statistical framework for massively parallel reporter assays T Ashuach, DS Fischer, A Kreimer, N Ahituv, FJ Theis, N Yosef Genome Biology 20 (1), 183, 2019 | 113 | 2019 |
| Group testing for SARS-CoV-2 allows for up to 10-fold efficiency increase across realistic scenarios and testing strategies CM Verdun, T Fuchs, P Harar, D Elbrächter, DS Fischer, J Berner, ... Frontiers in Public Health 9, 583377, 2021 | 85 | 2021 |
| 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 | 82 | 2022 |
| Programs, origins and immunomodulatory functions of myeloid cells in glioma TE Miller, CA El Farran, CP Couturier, Z Chen, JP D’Antonio, J Verga, ... Nature, 1-11, 2025 | 71* | 2025 |
| Toward modeling metabolic state from single-cell transcriptomics K Hrovatin, DS Fischer, FJ Theis Molecular Metabolism 57, 101396, 2022 | 62 | 2022 |
| Modeling fragment counts improves single-cell ATAC-seq analysis LD Martens, DS Fischer, VA Yépez, FJ Theis, J Gagneur Nature Methods, 1-4, 2023 | 59 | 2023 |
| Graph representation learning for single-cell biology L Hetzel, DS Fischer, S Günnemann, FJ Theis Current Opinion in Systems Biology 28, 100347, 2021 | 58 | 2021 |
| scTab: Scaling cross-tissue single-cell annotation models F Fischer, DS Fischer, R Mukhin, A Isaev, E Biederstedt, AC Villani, ... Nature Communications 15 (1), 6611, 2024 | 52* | 2024 |
Fabian J TheisHelmholtz Munich, Technical University of MunichVerified email at helmholtz-muenchen.de
