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
  <https://doi.org/10.1093/bioinformatics/btv359>.

A BibTeX entry for LaTeX users is

  @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},
  }

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
  <https://doi.org/10.1093/nar/gks457>.

A BibTeX entry for LaTeX users is

  @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},
  }

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
  <https://doi.org/10.3389/fimmu.2013.00358>.

A BibTeX entry for LaTeX users is

  @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},
  }

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
  <https://doi.org/10.4049/jimmunol.1502263>.

A BibTeX entry for LaTeX users is

  @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},
  }

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
  <https://doi.org/10.3389/fimmu.2018.01687>.

A BibTeX entry for LaTeX users is

  @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},
  }