genbioconductor.bib

@article{Bernstein:2006,
  author =	 {Bernstein, Bradley E and Mikkelsen, Tarjei S and Xie, Xiaohui and Kamal, Michael
                  and Huebert, Dana J and Cuff, James and Fry, Ben and Meissner, Alex and Wernig,
                  Marius and Plath, Kathrin and Jaenisch, Rudolf and Wagschal, Alexandre and Feil,
                  Robert and Schreiber, Stuart L and Lander, Eric S},
  title =	 {{A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem
                  Cells}},
  journal =	 {Cell},
  year =	 {2006},
  volume =	 {125},
  number =	 {2},
  pages =	 {315--326},
  doi =		 {10.1016/j.cell.2006.02.041}
}

@book{Durbin:1998,
  author =	 {Durbin, Richard M and Eddy, Sean R and Krogh, Anders and Mitchison, Graeme and
                  Eddy, Sean R},
  title =	 {{Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic
                  Acids}},
  publisher =	 {Cambridge University Press},
  year =	 {1998},
  isbn =	 {0521620414}
}


@article{Bioconductor,
  author =	 {Gentleman, Robert C and Carey, Vincent J and Bates, Douglas M and Bolstad, Ben and
                  Dettling, Marcel and Dudoit, Sandrine and Ellis, Byron and Gautier, Laurent and
                  Ge, Yongchao and Gentry, Jeff and Hornik, Kurt and Hothorn, Torsten and Huber,
                  Wolfgang and Iacus, Stefano and Irizarry, Rafael and Leisch, Friedrich and Li,
                  Cheng and Maechler, Martin and Rossini, Anthony J and Sawitzki, Gunther and Smith,
                  Colin and Smyth, Gordon and Tierney, Luke and Yang, Jean Y H and Zhang, Jianhua},
  title =	 {{Bioconductor: open software development for computational biology and
                  bioinformatics.}},
  journal =	 {Genome Biology},
  year =	 {2004},
  volume =	 {5},
  number =	 {10},
  pages =	 {R80},
  doi =		 {10.1186/gb-2004-5-10-r80},
  pmid =	 {15461798}
}

@article{BioconductorNew,
  author =	 {Huber, Wolfgang and Carey, Vincent J and Gentleman, Robert and Anders, Simon and
                  Carlson, Marc and Carvalho, Benilton S and Bravo, H{\'e}ctor Corrada and Davis,
                  Sean and Gatto, Laurent and Girke, Thomas and Gottardo, Raphael and Hahne, Florian
                  and Hansen, Kasper D and Irizarry, Rafael A and Lawrence, Michael and Love,
                  Michael I and MacDonald, James and Obenchain, Valerie and Ole{\'s}, Andrzej K and
                  Pag{\`e}s, Herv{\'e} and Reyes, Alejandro and Shannon, Paul and Smyth, Gordon K
                  and Tenenbaum, Dan and Waldron, Levi and Morgan, Martin},
  title =	 {{Orchestrating high-throughput genomic analysis with Bioconductor.}},
  journal =	 {Nature Methods},
  year =	 {2015},
  volume =	 {12},
  number =	 {2},
  pages =	 {115--121},
  doi =		 {10.1038/nmeth.3252},
  pmid =	 {25633503}
}

@article{GenomicRanges,
  author =	 {Lawrence, Michael and Huber, Wolfgang and Pag{\`e}s, Herv{\'e} and Aboyoun,
                  Patrick and Carlson, Marc and Gentleman, Robert and Morgan, Martin T and Carey,
                  Vincent J},
  title =	 {{Software for computing and annotating genomic ranges.}},
  journal =	 {PLoS Computational Biology},
  year =	 {2013},
  volume =	 {9},
  number =	 {8},
  pages =	 {e1003118},
  doi =		 {10.1371/journal.pcbi.1003118},
  pmid =	 {23950696}
}

@article{Hansen:EBV,
  author =	 {Kasper D Hansen and Sabunciyan, Sarven and Langmead, Ben and Nagy, Noemi and
                  Curley, Rebecca and Klein, Georg and Klein, Eva and Salamon, Daniel and Feinberg,
                  Andrew P},
  title =	 {{Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced
                  B-cell immortalization.}},
  journal =	 {Genome Research},
  year =	 {2014},
  volume =	 {24},
  number =	 {2},
  pages =	 {177--184},
  doi =		 {10.1101/gr.157743.113},
  pmid =	 {24068705}
}