To cite package ‘DEXSeq’ in publications use:

  Simon Anders, Alejandro Reyes and Wolfgang Huber (2012): Detecting
  differential usage of exons from RNA-seq data. Genome Research (2012)
  22:2008. doi:10.1101/gr.133744.111

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Detecting differential usage of exons from RNA-seq data.},
    author = {Simon Anders and Alejandro Reyes and Wolfgang Huber},
    year = {2012},
    journal = {Genome Research},
    volume = {22},
    pages = {4025},
    doi = {10.1101/gr.133744.111},
  }

  Alejandro Reyes, Simon Anders, et al (2013): Drift and conservation
  of differential exon usage across tissues in primate species. PNAS
  (2013) 110:15277. doi:10.1073/pnas.1307202110

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Drift and conservation of differential exon usage across tissues in primate species.},
    author = {Alejandro Reyes and Simon Anders and Robert Weatheritt and Toby Gibson and Lars Steinmetz and Wolfgang Huber},
    year = {2013},
    journal = {PNAS},
    volume = {110},
    pages = {-5},
    doi = {10.1073/pnas.1307202110},
  }