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>.

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>.

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>.

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.

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.

Corresponding BibTeX entries:

  @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},
  }

  @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},
  }

  @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},
  }

  @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},
  }