To cite the dowser package in publications, please use

Hoehn K, Pybus O, Kleinstein S (2022). “Phylogenetic analysis of migration, differentiation, and class switching in B cells.” PLoS Computational Biology. doi:10.1371/journal.pcbi.1009885, https://doi.org/10.1371/journal.pcbi.1009885.

If you use the [correlationTest](vignettes/Measurable-Evolution.md) function for measurable evolution, please also cite

Hoehn K, Turner J, Miller F, Jiang R, Ellebedy A, Pybus O, Kleinstein S (2021). “Human B cell lineages associated with germinal centers following influenza vaccination are measurably evolving.” eLife. doi:10.7554/eLife.70873, https://elifesciences.org/articles/70873.

If you construct [paired heavy and light chain trees](vignettes/Resolve-Light-Chains-Vignette.md), please also cite

Jensen C, Sumner J, Kleinstein S, Hoehn K (2024). “Inferring B Cell Phylogenies from Paired H and L Chain BCR Sequences with Dowser.” The Journal of Immunology. doi:10.4049/jimmunol.2300851, https://doi.org/10.4049/jimmunol.2300851.

If you additionally use [IgPhyML](https://igphyml.readthedocs.io) for building trees please also cite

Hoehn K, Van der Heiden J, Zhou J, Lunter G, Pybus O, Kleinstein S (2019). “Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination.” PNAS. doi:10.1073/pnas.1906020116, https://doi.org/10.1073/pnas.1906020116.

Corresponding BibTeX entries:

  @Article{,
    style = {citation},
    title = {Phylogenetic analysis of migration, differentiation, and
      class switching in B cells.},
    author = {Kenneth B. Hoehn and Oliver G. Pybus and Steven H.
      Kleinstein},
    year = {2022},
    journal = {PLoS Computational Biology},
    url = {https://doi.org/10.1371/journal.pcbi.1009885},
    doi = {10.1371/journal.pcbi.1009885},
  }

  @Article{,
    style = {citation},
    title = {Human B cell lineages associated with germinal centers
      following influenza vaccination are measurably evolving.},
    author = {Kenneth B. Hoehn and Jackson S. Turner and Frederick I.
      Miller and Ruoyi Jiang and Ali H. Ellebedy and Oliver G. Pybus
      and Steven H. Kleinstein},
    year = {2021},
    journal = {eLife},
    url = {https://elifesciences.org/articles/70873},
    doi = {10.7554/eLife.70873},
  }

  @Article{,
    style = {citation},
    title = {Inferring B Cell Phylogenies from Paired H and L Chain BCR
      Sequences with Dowser.},
    author = {Cole G. Jensen and Jacob A. Sumner and Steven H.
      Kleinstein and Kenneth B. Hoehn},
    year = {2024},
    journal = {The Journal of Immunology},
    url = {https://doi.org/10.4049/jimmunol.2300851},
    doi = {10.4049/jimmunol.2300851},
  }

  @Article{,
    style = {citation},
    title = {Repertoire-wide phylogenetic models of B cell molecular
      evolution reveal evolutionary signatures of aging and
      vaccination.},
    author = {Kenneth B. Hoehn and Jason A. {Van der Heiden} and Julian
      Q. Zhou and Gerton Lunter and Oliver G. Pybus and Steven H.
      Kleinstein},
    year = {2019},
    journal = {PNAS},
    url = {https://doi.org/10.1073/pnas.1906020116},
    doi = {10.1073/pnas.1906020116},
  }