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@Misc{morganrsamtools,
  Title                    = {Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import. R package version 1.18. 2},

  Author                   = {Morgan, M and Pag{\`e}s, H and Obenchain, V and Hayden, N}
}

@Article{desantiago2016,
  Title                    = {BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes},
  Author                   = {deSantiago, I and Liu, W and  Yuan, K and O'Reilly, M and Chilamakuri, CS and Ponder, BJ and Meyer, KM and Markowetz, F},
  Journal                  = {in press},
  Year                     = {2016},
  Number                   = {},
  Pages                    = {},
  Volume                   = {},

  Publisher                = {BioMed Central}
}

@Article{pickrell2011false,
  Title                    = {False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions},
  Author                   = {Pickrell, Joseph K and Gaffney, Daniel J and Gilad, Yoav and Pritchard, Jonathan K},
  Journal                  = {Bioinformatics},
  Year                     = {2011},
  Number                   = {15},
  Pages                    = {2144--2146},
  Volume                   = {27},

  Publisher                = {Oxford Univ Press}
}

@Article{encode2012integrated,
  Title                    = {An integrated encyclopedia of DNA elements in the human genome},
  Author                   = {ENCODE Project Consortium},
  Journal                  = {Nature},
  Year                     = {2012},
  Number                   = {7414},
  Pages                    = {57--74},
  Volume                   = {489},

  Publisher                = {Nature Publishing Group}
}

@Article{castel2015tools,
  Title                    = {Tools and best practices for data processing in allelic expression analysis},
  Author                   = {Castel, Stephane E and Levy-Moonshine, Ami and Mohammadi, Pejman and Banks, Eric and Lappalainen, Tuuli},
  Journal                  = {Genome biology},
  Year                     = {2015},
  Number                   = {1},
  Pages                    = {1},
  Volume                   = {16},

  Publisher                = {BioMed Central}
}

@Article{fujita2010ucsc,
  Title                    = {The UCSC genome browser database: update 2011},
  Author                   = {Fujita, Pauline A and Rhead, Brooke and Zweig, Ann S and Hinrichs, Angie S and Karolchik, Donna and Cline, Melissa S and Goldman, Mary and Barber, Galt P and Clawson, Hiram and Coelho, Antonio and others},
  Journal                  = {Nucleic acids research},
  Year                     = {2010},
  Pages                    = {gkq963},

  Publisher                = {Oxford Univ Press}
}


@Article{carroll2014impact,
  Title                    = {Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data},
  Author                   = {Carroll, Thomas S and Liang, Ziwei and Salama, Rafik and Stark, Rory and de Santiago, Ines},
  Journal                  = {Front Genet},
  Year                     = {2014},
  Pages                    = {75},
  Volume                   = {5}
}

@Article{lawrence2013software,
  Title                    = {Software for computing and annotating genomic ranges},
  Author                   = {Lawrence, Michael and Huber, Wolfgang and Pages, Herv{\'e} and Aboyoun, Patrick and Carlson, Marc and Gentleman, Robert and Morgan, Martin T and Carey, Vincent J},
  Journal                  = {PLoS Comput Biol},
  Year                     = {2013},
  Number                   = {8},
  Pages                    = {e1003118},
  Volume                   = {9},

  Publisher                = {Public Library of Science}
}

@Article{pickrell2010understanding,
  Title                    = {Understanding mechanisms underlying human gene expression variation with RNA sequencing},
  Author                   = {Pickrell, Joseph K and Marioni, John C and Pai, Athma A and Degner, Jacob F and Engelhardt, Barbara E and Nkadori, Everlyne and Veyrieras, Jean-Baptiste and Stephens, Matthew and Gilad, Yoav and Pritchard, Jonathan K},
  Journal                  = {Nature},
  Year                     = {2010},
  Number                   = {7289},
  Pages                    = {768--772},
  Volume                   = {464},

  Publisher                = {Nature Publishing Group}
}

@Article{kilpinen2013coordinated,
  Title                    = {Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription},
  Author                   = {Kilpinen, Helena and Waszak, Sebastian M and Gschwind, Andreas R and Raghav, Sunil K and Witwicki, Robert M and Orioli, Andrea and Migliavacca, Eugenia and Wiederkehr, Micha{\"e}l and Gutierrez-Arcelus, Maria and Panousis, Nikolaos I and others},
  Journal                  = {Science},
  Year                     = {2013},
  Number                   = {6159},
  Pages                    = {744--747},
  Volume                   = {342},

  Publisher                = {American Association for the Advancement of Science}
}

@Article{lappalainen2013transcriptome,
  Title                    = {Transcriptome and genome sequencing uncovers functional variation in humans},
  Author                   = {Lappalainen, Tuuli and Sammeth, Michael and Friedl{\"a}nder, Marc R and ACÔt Hoen, Peter and Monlong, Jean and Rivas, Manuel A and Gonz{\`a}lez-Porta, Mar and Kurbatova, Natalja and Griebel, Thasso and Ferreira, Pedro G and others},
  Journal                  = {Nature},
  Year                     = {2013},
  Number                   = {7468},
  Pages                    = {506--511},
  Volume                   = {501},

  Publisher                = {Nature Publishing Group}
}

@Article{degner2009effect,
  Title                    = {Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data},
  Author                   = {Degner, Jacob F and Marioni, John C and Pai, Athma A and Pickrell, Joseph K and Nkadori, Everlyne and Gilad, Yoav and Pritchard, Jonathan K},
  Journal                  = {Bioinformatics},
  Year                     = {2009},
  Number                   = {24},
  Pages                    = {3207--3212},
  Volume                   = {25},

  Publisher                = {Oxford Univ Press}
}

@Article{skelly2011powerful,
  Title                    = {A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data},
  Author                   = {Skelly, Daniel A and Johansson, Marnie and Madeoy, Jennifer and Wakefield, Jon and Akey, Joshua M},
  Journal                  = {Genome research},
  Year                     = {2011},
  Number                   = {10},
  Pages                    = {1728--1737},
  Volume                   = {21},

  Publisher                = {Cold Spring Harbor Lab}
}





