@Manual{pwmenrich,
    title = {PWMEnrich: PWM enrichment analysis},
    author = {Robert Stojnic and Diego Diez},
    year = {2015},
    note = {R package version 4.6.0},
}
@Manual{motifdb,
    title = {MotifDb: An Annotated Collection of Protein-DNA Binding 
            Sequence Motifs},
    author = {Paul Shannon},
    year = {2015},
    note = {R package version 1.12.1},
}
@article{rahmann,
    title={On the power of profiles for transcription factor binding 
            site detection},
    author={Rahmann, Sven and M{\"u}ller, Tobias and Vingron, Martin},
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    number={1},
    year={2003}
}
@article{encode2012,
    title={An integrated encyclopedia of DNA elements in the human genome},
    author={ENCODE Project Consortium and others},
    journal={Nature},
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    number={7414},
    pages={57--74},
    year={2012},
    publisher={Nature Publishing Group}
}

@article{reinert,
    title={Probabilistic and statistical properties of words: an overview},
    author={Reinert, Gesine and Schbath, Sophie and Waterman, Michael S},
    journal={Journal of Computational Biology},
    volume={7},
    number={1-2},
    pages={1--46},
    year={2000},
    publisher={Mary Ann Liebert, Inc.}
}
@article{zhang,
    title={Computing exact P-values for DNA motifs},
    author={Zhang, Jing and Jiang, Bo and Li, Ming and Tromp, John and Zhang, 
            Xuegong and Zhang, Michael Q},
    journal={Bioinformatics},
    volume={23},
    number={5},
    pages={531--537},
    year={2007},
    publisher={Oxford Univ Press}
}
@article{reinert,
    title={Probabilistic and statistical properties of words: an overview},
    author={Reinert, Gesine and Schbath, Sophie and Waterman, Michael S},
    journal={Journal of Computational Biology},
    volume={7},
    number={1-2},
    pages={1--46},
    year={2000},
    publisher={Mary Ann Liebert, Inc.}
}

@article{rsat1,
    title={RSAT: regulatory sequence analysis tools},
    author={Thomas-Chollier, Morgane and Sand, Olivier and Turatsinze,
            Jean-Val{\'e}ry and Defrance, Matthieu and Vervisch,
            Eric and Broh{\'e}e, Sylvain and van Helden, Jacques and others},
    journal={Nucleic acids research},
    volume={36},
    number={suppl 2},
    pages={W119--W127},
    year={2008},
    publisher={Oxford Univ Press}
}
@article{pape,
    title={Compound Poisson approximation of the number of occurrences
            of a position frequency matrix (PFM) on both strands},
    author={Pape, Utz J and Rahmann, Sven and Sun, Fengzhu and Vingron, Martin},
    journal={Journal of Computational Biology},
    volume={15},
    number={6},
    pages={547--564},
    year={2008},
}
@phdthesis{koppdiss,
    title={TBA},
    author={TBA},
    year={TBA},
    school={TBA}
}
