| CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets M Nowicka, C Krieg, HL Crowell, LM Weber, FJ Hartmann, S Guglietta, ... F1000Research 6, 748, 2019 | 513 | 2019 |
| Compensation of signal spillover in suspension and imaging mass cytometry HL Crowell, S Chevrier, VRT Zanotelli, S Engler, MD Robinson, ... Cell systems 6 (5), 612-620. e5, 2018 | 371* | 2018 |
| muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data HL Crowell, C Soneson, PL Germain, D Calini, L Collin, C Raposo, ... Nature communications 11 (1), 6077, 2020 | 322* | 2020 |
| Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease A Garrido-Trigo, AM Corraliza, M Veny, I Dotti, E Melón-Ardanaz, A Rill, ... Nature communications 14 (1), 4506, 2023 | 112 | 2023 |
| SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor HL Crowell, D Righelli, LM Weber, B Pardo, L Collado-Torres, ... Bioinformatics 38 (11), 3128-3131, 2022 | 103 | 2022 |
| CATALYST: Cytometry dATa anALYSis Tools HL Crowell, VRT Zanotelli, S Chevrier, MD Robinson, B Bodenmiller R package, Bioconductor, 2017 | 80* | 2017 |
| An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data HL Crowell, S Chevrier, A Jacobs, S Sivapatham, B Bodenmiller, ... F1000Research 9, 1263, 2022 | 47 | 2022 |
| CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data A Lütge, J Zyprych-Walczak, UB Kunzmann, HL Crowell, D Calini, ... Life science alliance 4 (6), 2021 | 39 | 2021 |
| The shaky foundations of simulating single-cell RNA sequencing data HL Crowell, SX Morillo Leonardo, C Soneson, MD Robinson Genome Biology 24 (1), 62, 2023 | 36* | 2023 |
| Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma KD Prummel, HL Crowell, S Nieuwenhuize, EC Brombacher, S Daetwyler, ... Nature Communications 13 (1), 1677, 2022 | 27 | 2022 |
| Feedback mechanisms control coexistence in a stem cell model of acute myeloid leukaemia HL Crowell, AL MacLean, MPH Stumpf Journal of Theoretical Biology 401, 43-53, 2016 | 22 | 2016 |
| distinct: A novel approach to differential distribution analyses S Tiberi, HL Crowell, P Samartsidis, LM Weber, MD Robinson The Annals of Applied Statistics 17 (2), 1681-1700, 2023 | 21 | 2023 |
| Predicting neurological recovery after traumatic spinal cord injury by time-resolved analysis of monocyte subsets RA Heller, J Seelig, HL Crowell, M Pilz, P Haubruck, Q Sun, L Schomburg, ... Brain 144 (10), 3159-3174, 2021 | 18 | 2021 |
| The tidyomics ecosystem: Enhancing omic data analyses WJ Hutchison, TJ Keyes, Tidyomics Consortium, HL Crowell, J Serizay, ... Nature Methods, 1-5, 2024 | 11 | 2024 |
| Selenium-binding protein 1 (SELENBP1) as biomarker for adverse clinical outcome after traumatic spinal cord injury J Seelig, RA Heller, P Haubruck, Q Sun, GJ Klingenberg, J Hackler, ... Frontiers in neuroscience 15, 680240, 2021 | 11 | 2021 |
| Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability A Sonrel, A Luetge, C Soneson, I Mallona, PL Germain, S Knyazev, J Gilis, ... Genome Biology 24 (1), 119, 2023 | 10 | 2023 |
| pasta: Pattern Analysis for Spatial Omics Data M Emons, S Gunz, HL Crowell, I Mallona, R Furrer, MD Robinson arXiv preprint arXiv:2412.01561, 2024 | | 2024 |
| STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging E Pitino, A Pascual-Reguant, F Segato-Dezem, K Wise, ... bioRxiv, 2024.10. 03.616013, 2024 | | 2024 |
| Disentangling cell type and state transcriptional programs J Wang, HL Crowell, MD Robinson bioRxiv, 2024.11. 29.626057, 2024 | | 2024 |
| Computational methods development and benchmarking for single-cell and spatial resolved omics data HL Crowell University of Zurich, 2023 | | 2023 |