To cite the SHazaM package in publications, please use:

Gupta N, Vander Heiden J, Uduman M, Gadala-Maria D, Yaari G, Kleinstein S (2015). “Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data.” Bioinformatics, 1-3. doi:10.1093/bioinformatics/btv359.

To cite the selection analysis methods, please use:

Yaari G, Uduman M, Kleinstein S (2012). “Quantifying selection in high-throughput Immunoglobulin sequencing data sets.” Nucleic acids research, 40(17), e134. doi:10.1093/nar/gks457.

To cite the HH_S5F model and the targeting model generation methods, please use:

Yaari G, Vander Heiden J, Uduman M, Gadala-Maria D, Gupta N, Stern J, O'Connor K, Hafler D, Lasserson U, Vigneault F, Kleinstein S (2013). “Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data.” Frontiers in Immunology, 4(358), 1-11. doi:10.3389/fimmu.2013.00358.

To cite the HKL_S1F, HKL_S5F, MK_RS1NF, and MK_RS5NF models, please use:

Cui A, Di Niro R, Vander Heiden J, Briggs A, Adams K, Gilbert T, O'Connor K, Vigneault F, Shlomchik M, Kleinstein S (2016). “A Model of Somatic Hypermutation Targeting in Mice Based on High-Throughput Ig Sequencing Data.” The Journal of Immunology, 197(9), 3566-3574. doi:10.4049/jimmunol.1502263.

To cite the mixture model for threshold determination, please use:

Nouri N, Kleinstein S (2018). “Optimized Threshold Inference for Partitioning of Clones From High-Throughput B Cell Repertoire Sequencing Data.” Frontiers in Immunology, 9. doi:10.3389/fimmu.2018.01687.

Corresponding BibTeX entries:

  @Article{,
    style = {citation},
    title = {Change-O: a toolkit for analyzing large-scale B cell
      immunoglobulin repertoire sequencing data.},
    author = {Namita T. Gupta and Jason A. {Vander Heiden} and Mohamed
      Uduman and Daniel Gadala-Maria and Gur Yaari and Steven H.
      Kleinstein},
    year = {2015},
    journal = {Bioinformatics},
    pages = {1-3},
    doi = {10.1093/bioinformatics/btv359},
  }

  @Article{,
    style = {citation},
    title = {Quantifying selection in high-throughput Immunoglobulin
      sequencing data sets.},
    author = {Gur Yaari and Mohamed Uduman and Steven H. Kleinstein},
    year = {2012},
    journal = {Nucleic acids research},
    volume = {40},
    number = {17},
    pages = {e134},
    doi = {10.1093/nar/gks457},
  }

  @Article{,
    style = {citation},
    title = {Models of somatic hypermutation targeting and substitution
      based on synonymous mutations from high-throughput immunoglobulin
      sequencing data.},
    author = {Gur Yaari and Jason A. {Vander Heiden} and Mohamed Uduman
      and Daniel Gadala-Maria and Namita T. Gupta and Joel N. H. Stern
      and Kevin C. O'Connor and David A. Hafler and Uri Lasserson and
      Francois Vigneault and Steven H. Kleinstein},
    year = {2013},
    journal = {Frontiers in Immunology},
    volume = {4},
    number = {358},
    pages = {1-11},
    doi = {10.3389/fimmu.2013.00358},
  }

  @Article{,
    style = {citation},
    title = {A Model of Somatic Hypermutation Targeting in Mice Based
      on High-Throughput Ig Sequencing Data.},
    author = {Ang Cui and Roberto {Di Niro} and Jason A. {Vander
      Heiden} and Adrian W. Briggs and Kris Adams and Tamara Gilbert
      and Kevin C. O'Connor and Francois Vigneault and Mark J.
      Shlomchik and Steven H. Kleinstein},
    year = {2016},
    journal = {The Journal of Immunology},
    volume = {197},
    number = {9},
    pages = {3566-3574},
    doi = {10.4049/jimmunol.1502263},
  }

  @Article{,
    style = {citation},
    title = {Optimized Threshold Inference for Partitioning of Clones
      From High-Throughput B Cell Repertoire Sequencing Data},
    author = {Nima Nouri and Steven H. Kleinstein},
    year = {2018},
    journal = {Frontiers in Immunology},
    volume = {9},
    doi = {10.3389/fimmu.2018.01687},
  }