Crowell, L H, Soneson, Charlotte, Germain, Pierre-Luc, Calini, Daniela, Collin, Ludovic, Raposo, Catarina, Malhotra, Dheeraj, Robinson, D M (2020). “muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data.” Nature Communications, 11(1), 6077. doi:10.1038/s41467-020-19894-4.

Gilis, Jeroen, Perin, Laura, Malfait, Milan, Crowell, L H, Van den Berge, Koen, Assefa, Takele A, Verbist, Bie, Risso, Davide, Clement, Lieven (2025). “Differential detection workflows for multi-sample single-cell RNA-seq data.” BMC Genomics, 26(1), 886. doi:10.1186/s12864-025-12102-x.

Germain, Pierre-Luc, Wang, Jiayi, Robinson, D M (2025). “Bulk-based hypothesis weighing increases power in single-cell differential expression analysis.” Peer Community Journal, 5(e136). doi:10.24072/pcjournal.663.

Corresponding BibTeX entries:

  @Article{,
    title = {muscat detects subpopulation-specific state transitions
      from multi-sample multi-condition single-cell transcriptomics
      data},
    author = {{Crowell} and Helena L and {Soneson} and {Charlotte} and
      {Germain} and {Pierre-Luc} and {Calini} and {Daniela} and
      {Collin} and {Ludovic} and {Raposo} and {Catarina} and {Malhotra}
      and {Dheeraj} and {Robinson} and Mark D},
    journal = {Nature Communications},
    volume = {11},
    number = {1},
    pages = {6077},
    year = {2020},
    doi = {10.1038/s41467-020-19894-4},
  }

  @Article{,
    title = {{Differential detection workflows for multi-sample
      single-cell RNA-seq data}},
    author = {{Gilis} and {Jeroen} and {Perin} and {Laura} and
      {Malfait} and {Milan} and {Crowell} and Helena L and {Van den
      Berge} and {Koen} and {Assefa} and Alemu Takele and {Verbist} and
      {Bie} and {Risso} and {Davide} and {Clement} and {Lieven}},
    journal = {BMC Genomics},
    volume = {26},
    number = {1},
    pages = {886},
    year = {2025},
    doi = {10.1186/s12864-025-12102-x},
  }

  @Article{,
    title = {Bulk-based hypothesis weighing increases power in
      single-cell differential expression analysis},
    author = {{Germain} and {Pierre-Luc} and {Wang} and {Jiayi} and
      {Robinson} and Mark D},
    journal = {Peer Community Journal},
    year = {2025},
    volume = {5},
    number = {e136},
    doi = {10.24072/pcjournal.663},
  }