Publications

(\(\ast\) co-first. \(\dagger\) co-senior. correspondence.)

  • HL Crowell\(^\ast\), Y Dong\(^\ast\), I Billato, P Cai, M Emons, S Gunz, B Guo, M Li, A Mahmoud, A Manukyan, H Pagès, P Panwar, S Rao, CJ Sargeant, L Shepherd Kern, M Ramos, J Sun, M Totty, VJ Carey, Y Chen, L Collado-Torres, S Ghazanfar, KD Hansen, K Martinowich, KR Maynard, E Patrick, D Righelli, D Risso, S Tiberi, L Waldron, R Gottardo\(^\dagger\), MD Robinson\(^\dagger\), SC Hicks\(^\dagger\), LM Weber\(^\dagger\). Orchestrating spatial transcriptomics analysis with Bioconductor. bioRxiv (2025)

  • HL Crowell, L Llaó-Cid, G Frigola, S Gunz, P Lorden, M Ruiz, I Ruano, M Kulis, JI Martin-Subero, H Heyn, E Campo, A Pascual-Reguant. A transcriptional map of human tonsil architecture: beyond the sum of (single cell) parts. bioRxiv (2025)

  • HL Crowell, I Ruano, Z Hu, Y Hong, G Caratù, H Piessevaux, A Heck, R Liu, M Walter, M Vandenberg, K Young, D McGuire, E Metzger, ML Hoang, JM Beechem, S Tejpar, A Pascual-Reguant\(^\ast\), H Heyn\(^\ast\). Tracing colorectal malignancy transformation from cell to tissue scale. bioRxiv (2025)

  • J Wang\(^\ast\), HL Crowell\(^\ast\), MD Robinson\(^\ast\). On feature selection to disentangle cell type and state transcriptional programs. BMC Genomics 26, 1006 (2025)

  • HL Crowell, SX Morillo Leonardo, C Soneson, MD Robinson. The shaky foundations of simulating single-cell RNA sequencing data. Genome Biology 24, 62 (2023)

  • D Righelli\(^\ast\), HL Crowell\(^\ast\), LM Weber\(^\ast\), B Pardo, L Collado-Torres, S Ghazanfar, ATL Lun, SC Hicks\(^\dagger\), D Risso\(^\dagger\). SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor. Bioinformatics 38, 3128-3131 (2022)

  • HL Crowell\(^\ast\), S Chevrier\(^\ast\), A Jacobs, S Sivapatham, Tumor Profiler Consortium, B Bodenmiller\(^\dagger\), MD Robinson\(^\dagger\). An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data. F1000Research 9, 1263.v2 (2022)

  • HL Crowell, C Soneson, P-L Germain, D Calini, L Collin, C Raposo, D Malhotra, MD Robinson. muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data. Nature Communications 11, 6077 (2020)

  • S Chevrier\(^\ast\), HL Crowell\(^\ast\), VRT Zanotelli\(^\ast\), S Engler, MD Robinson, B Bodenmiller. Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry. Cell Systems 6, 612–620.e5 (2018)

  • Crowell HL, MacLean AL, Stumpf MPH. Feedback mechanisms control coexistence in a stem cell model of acute myeloid leukaemia. Journal of Theoretical Biology 401, 43-53 (2016)

Collaborations

  • S Gunz\(^\ast\), HL Crowell, MD Robinson. Analysis of anatomical multi-cellular structures from spatial omics data using sosta. bioRxiv (2025)

  • J Gilis, L Perin, M Malfait, HL Crowell, K Van den Berge, AT Assefa, B Verbist, D Risso, L Clement. Differential detection workflows for multi-sample single-cell RNA-seq data. BMC Genomics 26, 886 (2025)

  • M Emons\(^\ast\), S Gunz\(^\ast\), HL Crowell, I Mallona, R Furrer, MD Robinson. Harnessing the potential of spatial statistics for spatial omics data with pasta. Nucleic Acids Research 53, gkaf870 (2025)

  • A Jensen, HL Crowell, A Pascual-Reguant, I Ruano, S Tejpar, H Heyn, M Nilsson, S Marco Salas. In Situ Inference of Copy Number Variations in Image-Based Spatial Transcriptomics. bioRxiv (2025)

  • E Pitino\(^\ast\), A Pascual-Reguant\(^\ast\), F Segato-Dezem\(^\ast\), K Wise, I Salvador-Martinez, HL Crowell, E Courtois, WF Flynn, S Sivajothi, E Soja, S Ruiz, G Caratù, AE Sullivan, German Atzin Mora Roldan, BK Dredge, M Marção, Y Liu, H Chasteen, M Mohenska, J Polo, JC Nieto, J Plummer\(^\dagger\), H Heyn\(^\dagger\), L Martelotto\(^\dagger\). STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging. Cell (2025)

  • A Garrido-Trigo, AM Corraliza, M Veny, I Dotti, E Melon-Ardanaz, A Rill, HL Crowell, Á Corbí, V Gudiño, M Esteller, I Álvarez-Teubel, D Aguilar, MC Masamunt, E Killingbeck, Y Kim, M Leon, S Visvanathan, D Marchese, G Caratù, A Martin-Cardona, M Esteve, J Panés, E Ricart, E Mereu\(^\ast\), H Heyn\(^\ast\), A Salas. Macrophage and neutrophil heterogeneity at single-cell spatial resolution in inflammatory bowel disease. Nature Communications 14, 4506 (2023)

  • A Sonrel\(^\ast\), A Luetge\(^\ast\), C Soneson\(^\ast\), IM Gonzalez\(^\ast\), PL Germain, S Knyazev, J Gilis, R Gerber, R Seurinck, D Paul, E Sonder, HL Crowell, I Fanaswala, A Al-Ajami, E Heidari, S Schmeing, S Milosavljevic, Y Saeys, S Mangul, MD Robinson. Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability. Genome Biology 24, 119 (2023)

  • S Tiberi, HL Crowell, P Samartsidis, LM Weber, MD Robinson. distinct: a novel approach to differential distribution analyses. Annals of Applied Statistics 17(2):1681-1700 (2023)

  • KD Prummel, HL Crowell, S Nieuwenhuize, EC Brombacher, S Daetwyler, C Soneson, J Kresoja-Rakic, A Kocere, M Ronner, A Ernst, Z Labbaf, DE Clouthier, AB Firulli, H Sánchez-Iranzo, SR Naganathan, R O’Rourke, E Raz, N Mercader, A Burger, E Felley-Bosco, J Huisken, MD Robinson, C Mosimann. Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma. Nature Communications 13, 1677 (2022)

  • RA Heller, J Seelig, HL Crowell, M Pilz, P Haubruck, Q Sun, L Schomburg, V Daniel, A Moghaddam, B Biglari. Predicting neurological recovery after traumatic spinal cord injury by time-resolved analysis of monocyte subsets. Brain 144, 3159 (2021)

  • A Lütge, J Zyprych-Walczak, UB Kunzmann, HL Crowell, D Calini, D Malhotra, C Soneson, MD Robinson. CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data Life Science Alliance 6, e202001004 (2021)

  • J Seelig\(^\ast\), RA Heller\(^\ast\), P Haubruck, Q Sun, GJ Klingenberg, J Hackler, HL Crowell, V Daniel, A Moghaddam, L Schomburg, B Biglari. Selenium-binding protein 1 (SELENBP1) as biomarker for adverse clinical outcome after traumatic spinal cord injury. Frontiers in Neuroscience 15, 680240 (2021)

  • M Nowicka, C Krieg, HL Crowell, LM Weber, FJ Hartmann, S Guglietta, B Becher, MP Levesque, MD Robinson. CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets. F1000Research 6, 748.v4 (2019)

Conferences

Software

  • OSTA Bioc
    Orchestrating Spatial Transcriptomics Analysis with Bioconductor.
    Crowell HL, Y Dong, R Gottardo, Robinson MD, Hicks SC, Weber LM (2025).

  • CATALYST Bioc
    Preprocessing of and differential discovery in cytometry data.
    Crowell HL, Zanotelli VRT, Chevrier S, Robinson MD (2017).

  • muscat Bioc
    Multi-sample multi-group scRNA-seq data analysis tools.
    Crowell HL, Germain P-L, Soneson C, Sonrel A,
    Gilis J, Risso D, Clemend L, Robinson MD (2019).

  • SpatialExperiment Bioc
    S4 Class for Spatially Resolved Transcriptomics Data.
    Righelli D, Risso D, Crowell HL, Weber LM (2020).

  • SPOTlight Bioc
    Spatial transcriptomics deconvolution using a seeded NMF approach.
    Elosua-Bayes M, Crowell HL

Vitae

Experience

  • Postdoctoral Fellow, CNAG Barcelona, Spain (Sept. 2023+)
  • Bioconductor Technical Advisory board (2023+)
  • Postdoctoral Fellow, University of Zurich, Switzerland (June-Aug. 2023)
  • Consultancy, BioMed X Heidelberg, Germany (Nov.-Dec. ’24)
  • Consultancy, University of Kansas, USA (Apr.-July ’23)
  • Consultancy, EMBL Heidelberg, Germany (Aug.-Nov. ’22)
  • Bioconductor package reviewer (2021+)
  • Research Assistant, University of Zurich, Switzerland (2016-2018)

Education

  • PhD Epidemiology & Biostatistics, University of Zurich, Switzerland (2018-2023)
  • MSc Computation Biology & Bioinformatics, ETH Zurich, Switzerland (2015-2018)
  • BSc Biochemistry, University of Heidelberg, Germany (2012-2015)

Funding

  • SNSF Postdoc.Mobility, CNAG Barcelona, Spain (Sept. 2023+)
  • SNSF Doc.Mobility, CNAG Barcelona, Spain (2021-2022)
  • Erasmus scholarship, Imperial College London, UK (2014-2015)
  • RISE grant, Pennsylvania State University, USA (2014)

Honors

  • PhD distinction Faculty of Science, University of Zurich, Switzerland (2020)
  • Bioconductor community award Bioconductor Conference, virtual (2020)

Teaching