| 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 | 609 | 2022 |
| Best practices for single-cell analysis across modalities L Heumos, AC Schaar, C Lance, A Litinetskaya, F Drost, L Zappia, ... Nature Reviews Genetics, 1-23, 2023 | 553 | 2023 |
| Modeling intercellular communication in tissues using spatial graphs of cells DS Fischer, AC Schaar, FJ Theis Nature Biotechnology 41 (3), 332-336, 2023 | 158* | 2023 |
| 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, 1-3, 2023 | 140 | 2023 |
| Systemic alterations in neutrophils and their precursors in early-stage chronic obstructive pulmonary disease TS Kapellos, K Baßler, W Fujii, C Nalkurthi, AC Schaar, L Bonaguro, ... Cell reports 42 (6), 2023 | 25 | 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 | 12 | 2024 |
| Probe set selection for targeted spatial transcriptomics LB Kuemmerle, MD Luecken, AB Firsova, L Barros de Andrade e Sousa, ... Nature methods, 1-11, 2024 | 10 | 2024 |
| Single-cell Best Practices C., Schiller HB, and Theis FJ. 2023 L Heumos, AC Schaar, C Lance, A Litinetskaya, F Drost, L Zappia, ... Best practices for single-cell analysis across modalities. Nat Rev Genet 24 …, 0 | 7 | |
| 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 | 3 | 2024 |
| Considerations for building and using integrated single-cell atlases K Hrovatin, L Sikkema, VA Shitov, G Heimberg, M Shulman, AJ Oliver, ... Nature Methods, 1-17, 2024 | 2 | 2024 |
| Spatial transcriptomics (ST) of cigarette smoke (CS)-induced experimental COPD H Chen, I Galvao, C Donovan, R Kim, D Ortega, S Idrees, ... European Respiratory Journal 60 (suppl 66), 2022 | | 2022 |
| SpatialSSL: Whole-Brain Spatial Transcriptomics in the Mouse Brain with Self-Supervised Learning T Richter, A Schaar, F Drummer, CW Liao, L Endres, FJ Theis NeurIPS 2023 AI for Science Workshop, 0 | | |