@article{Core2008,
  author = {Leighton J. Core and Joshua J. Waterfall and John T. Lis},
  title = {Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at
    Human Promoters.},
  journal = {Science},
  year = {2008},
  volume = {322},
  pages = {1845--1848},
}

@article{Hah2011,
  author = {Nasun Hah and Charles G. Danko and Leighton Core and Joshua J. Waterfall
     and Adam Siepel and John T. Lis and W. Lee Kraus},
  title = {A Rapid, Extensive, and Transient Transcriptional Response to Estrogen
    Signaling in Breast Cancer Cells.},
  journal = {Cell},
  year = {2011},
  volume = {145},
  pages = {622--634},
}

@article{Hah2013,
    author = {Nasun Hah and Shino Murakami and Anusha Nagari and Charles G. Danko and W. Lee Kraus},
    title = {Enhancer transcripts mark active estrogen receptor binding sites.},
    year = {2009},
    journal = {Genome Res},
    volume = {23},
    pages = {1210--1223},
}

@article{Luo2014,
    author = {Xin Luo and Minho Chae and Raga Krishnakumar and Charles G. Danko and W. Lee Kraus},
    title = {Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFα
        signaling revealed by integrated genomic analyses.},
    year = {2014},
    journal = {BMC Genomics},
    volume = {24},
    pages = {155}
}

@article{Danko2013,
  author = {Charles G. Danko and Nasun Hah and Xin Luo and Andre L. Martins and Leighton Core
    and John T. Lis and Adam Siepel and W. Lee Kraus},
  title = {Signaling Pathways Differentially Affect RNA Polymerase II Initiation,
    Pausing and Elongation Rate in Cells.},
  journal = {Molecular Cell},
  year = {2013},
  volume = {50},
  pages = {212--222},
}

@article{Robinson2010,
  author = {Mark D. Robinson and Davis J. McCarthy and Gordon K. Smyth},
  title = {edgeR: a Bioconductor package for differential expression analysis of digital
    gene expression data.},
  journal = {Bioinformatics},
  year = {2010},
  volume = {26},
  pages = {139--140},
}

@article{Michael2009,
    author = {Michael Lawrence and Robert Gentleman and Vincent Carey},
    title = {rtracklayer: an R package for interfacing with
                  genome browsers.},
    year = {2009},
    journal = {Bioinformatics},
    volume = {25},
    pages = {1841--1842},
}

@MANUAL{PagesGRanges,
    author = {Marc Carlson and Patrick Aboyoun and Herve Pages},
    title = {An Introduction to GenomicRanges},
    note = {R package version 1.14.4},
}

@MANUAL{PagesIRanges,
    author = {H. Pages and P. Aboyoun and M. Lawrence},
    title = {IRanges: Infrastructure for manipulating intervals on sequences},
    note = {R package version 1.20.6},
}

@MANUAL{CarsonGFeatures,
    author = {M. Carlson and H. Pages and P. Aboyoun and S. Falcon and M. Morgan and D. Sarkar and M. Lawrence},
    title = {GenomicFeatures: Tools for making and manipulating transcript centric annotations},
    note = {R package version 1.14.2},
}
