To cite the alakazam 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 Ig-specific lineage reconstruction and diversity methods, please use:

Stern J, Yaari G, Vander Heiden J, Church G, Donahue W, Hintzen R, Huttner A, Laman J, Nagra R, Nylander A, Pitt D, Ramanan S, Siddiqui B, Vigneault F, Kleinstein S, Hafler D, O'Connor K (2014). “B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes.” Science Translational Medicine, 6(248), 248ra107. doi: 10.1126/scitranslmed.3008879.

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 = {B cells populating the multiple sclerosis brain mature in
      the draining cervical lymph nodes.},
    author = {Joel N. H. Stern and Gur Yaari and Jason A. {Vander
      Heiden} and George Church and William F. Donahue and Rogier Q.
      Hintzen and Anita J. Huttner and Jon D. Laman and Rashed M. Nagra
      and Alyssa Nylander and David Pitt and Sriram Ramanan and Bilal
      A. Siddiqui and Francois Vigneault and Steven H. Kleinstein and
      David A. Hafler and Kevin C. O'Connor},
    year = {2014},
    journal = {Science Translational Medicine},
    number = {248},
    volume = {6},
    pages = {248ra107},
    doi = {10.1126/scitranslmed.3008879},
  }