The puma package is based on a large body of methodological research.
Citing puma in publications will usually involve citing one or more of
the methodology papers that the software is based on as well as citing
the software package itself. For the methodology papers, see
http://www.bioinf.manchester.ac.uk/resources/puma/.  puma makes use of
the donlp2() function by Peter Spellucci. The use of donlp2() must be
acknowledged in any publication which contains results obtained with
puma or parts of it. Citation of the author's name and netlib-source is
suitable. The puma software itself as well as the extension of PPLR to
the multi-factorial case (the pumaDE function) can be cited as:

  puma: a Bioconductor package for Propagating Uncertainty in
  Microarray Analysis (2008) Pearson et al. In preparation

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Pearson et al},
    title = {puma: a Bioconductor package for Propagating Uncertainty in Microarray Analysis},
    journal = {in preparation},
    year = {2008},
  }

  puma3.0: improved uncertainty propagation methods for gene and
  transcirpt expression and analysis. (2013) Xuejun Liu,Zhenzhu Gao,Li
  Zhang BMC Bioinformatics

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Xuejun Liu,Zhenzhu Gao,Li Zhang},
    title = {puma3.0: improved uncertainty propagation methods for gene and transcirpt expression and analysis.},
    journal = {BMC Bioinformatics},
    year = {2013},
  }

  P. Spelluci. ANSI C-version of donlp2().
  http://plato.asu.edu/ftp/donlp2/donlp2_intv_dyn.tar.gz.

A BibTeX entry for LaTeX users is

  @Misc{,
    author = {P. Spelluci},
    title = {ANSI-C version of donlp2()},
    howpublished = {http://plato.asu.edu/ftp/donlp2/donlp2_intv_dyn.tar.gz},
  }

This free open-source software implements academic research by the
authors and co-workers. If you use it, please support the project by
citing the appropriate journal articles.