The tigre package is based on a body of methodological research.  The
software itself can be cited as:

  Antti Honkela, Pei Gao, Jonatan Ropponen, Magnus Rattray, and Neil D.
  Lawrence. tigre: Transcription factor Inference through Gaussian
  process Reconstruction of Expression for Bioconductor. Bioinformatics
  27(7):1026-1027, 2011. DOI: 10.1093/bioinformatics/btr057.

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Antti Honkela and Pei Gao and Jonatan Ropponen and Magnus Rattray and Neil D Lawrence},
    title = {tigre: Transcription factor Inference through Gaussian process Reconstruction of Expression for Bioconductor},
    journal = {Bioinformatics},
    year = {2011},
    volume = {27},
    pages = {1026-1027},
    number = {7},
    doi = {10.1093/bioinformatics/btr057},
    url = {http://dx.doi.org/10.1093/bioinformatics/btr057},
  }

The underlying methodology papers can be cited as:

  Antti Honkela, Charles Girardot, E. Hilary Gustafson, Ya-Hsin Liu,
  Eileen E. M. Furlong, Neil D. Lawrence, and Magnus Rattray.
  Model-based method for transcription factor target identification
  with limited data. Proc Natl Acad Sci USA 107(17):7793-7798, 2010.
  DOI: 10.1073/pnas.0914285107.

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Antti Honkela and Charles Girardot and E. Hilary Gustafson and Ya-Hsin Liu and Eileen E.M. Furlong and Neil D. Lawrence and Magnus Rattray},
    title = {Model-based method for transcription factor target identification with limited data},
    journal = {Proc Natl Acad Sci USA},
    year = {2010},
    volume = {107},
    pages = {7793-7798},
    number = {17},
    doi = {10.1073/pnas.0914285107},
    url = {http://dx.doi.org/10.1073/pnas.0914285107},
  }

Pei Gao, Antti Honkela, Magnus Rattray, and Neil D. Lawrence. Gaussian
process modelling of latent chemical species: applications to inferring
transcription factor activities. Bioinformatics 24(16):i70-i75, 2008.
DOI: 10.1093/bioinformatics/btn278.

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Pei Gao and Antti Honkela and Magnus Rattray and Neil D Lawrence},
    title = {Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities},
    journal = {Bioinformatics},
    year = {2008},
    volume = {24},
    pages = {i70-i75},
    number = {16},
    doi = {10.1093/bioinformatics/btn278},
  }

Neil D. Lawrence, Guido Sanguinetti, and Magnus Rattray. Modelling
transcriptional regulation using Gaussian processes. In B. Scholkopf,
J. C. Platt, and T. Hofmann, editors, Advances in Neural Information
Processing Systems, volume 19, pages 785-792. MIT Press, Cambridge, MA,
2007.

A BibTeX entry for LaTeX users is

  @InCollection{,
    author = {Neil D. Lawrence and Guido Sanguinetti and Magnus Rattray},
    title = {Modelling transcriptional regulation using {G}aussian processes},
    booktitle = {Advances in Neural Information Processing Systems},
    publisher = {MIT Press},
    year = {2007},
    editor = {B. Sch\"{o}lkopf and J. C. Platt and T. Hofmann},
    volume = {19},
    pages = {785-792},
    address = {Cambridge, MA},
  }

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.