@Article{Anders:2010:GB,
  url =		 {http://genomebiology.com/2010/11/10/R106},
  author =	 {Simon Anders and Wolfgang Huber},
  Title =	 {{D}ifferential expression analysis for sequence
                  count data},
  Journal =	 {Genome Biology},
  Year =	 2010,
  Volume =	 11,
  Pages =	 {R106},
}

@Article{Bourgon:2010:PNAS,
  ISI =		 {ISI:000278054700015},
  URL =		 {http://www.pnas.org/content/107/21/9546.long},
  PDF =		 {PNAS-2010-Bourgon-9546-51.pdf},
  author =	 {Richard Bourgon and Robert Gentleman and Wolfgang
                  Huber},
  Title =	 {Independent filtering increases detection power for
                  high-throughput experiments},
  journal =	 {PNAS},
  Year =	 2010,
  volume =	 107,
  number =	 21,
  pages =	 {9546--9551},
}

@article{Brooks2010,
  author =	 {Brooks, A. N. and Yang, L. and Duff, M. O. and
                  Hansen, K. D. and Park, J. W. and Dudoit, S. and
                  Brenner, S. E. and Graveley, B. R.},
  doi =		 {10.1101/gr.108662.110},
  issn =	 {1088-9051},
  journal =	 {Genome Research},
  pages =	 {193--202},
  title =	 {{Conservation of an RNA regulatory map between
                  Drosophila and mammals}},
  url =
                  {http://genome.cshlp.org/cgi/doi/10.1101/gr.108662.110},
  year =	 2011
}

@misc{htseq,
  author =	 {Simon Anders},
  title =	 {{HTSeq: Analysing high-throughput sequencing data
                  with Python}},
  year =	 2011,
  howpublished = {\url{http://www-huber.embl.de/users/anders/HTSeq/}}
}

@misc{summerizeOverlaps,
  author =	 {Valerie Obenchain},
  title =	 {Counting with \texttt{summarizeOverlaps}},
  year =	 2011,
  howpublished = {Vignette, distributed as part of the Bioconductor
                  package \emph{GenomicRanges}, as file
                  \emph{summarizeOverlaps.pdf}}
}
