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\begin{thebibliography}{}
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\newblock Transposition of native chromatin for fast and sensitive epigenomic
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\newblock Positional specificity of different transcription factor classes
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\newblock {JASPAR} 2018: update of the open-access database of transcription
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\newblock {SC}3: consensus clustering of single-cell {RNA}-seq data.
\newblock {\em Nature Methods}, 14(5):483--486.
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V.~B., Papatsenko, D.~A., Kolpakov, F.~A., and Makeev, V.~J. (2018).
\newblock {HOCOMOCO}: towards a complete collection of transcription factor
binding models for human and mouse via large-scale {ChIP}-{Seq} analysis.
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Sidow, A. (2012).
\newblock Ubiquitous heterogeneity and asymmetry of the chromatin environment
at regulatory elements.
\newblock {\em Genome Research}, 22(9):1735--1747.
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\newblock Ultrafast and memory-efficient alignment of short {DNA} sequences to
the human genome.
\newblock {\em Genome Biology}, 10(3):R25.
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\newblock Identification of transcription factor binding sites using
{ATAC}-seq.
\newblock {\em Genome Biology}, 20(1):45.
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Nair, N.~U., Kumar, S., Moret, B. M.~E., and Bucher, P. (2014).
\newblock Probabilistic partitioning methods to find significant patterns in
{ChIP}-{Seq} data.
\newblock {\em Bioinformatics}, 30(17):2406--2413.
\bibitem[Neph et~al., 2012]{neph_expansive_2012}
Neph, S., Vierstra, J., Stergachis, A.~B., Reynolds, A.~P., Haugen, E., Vernot,
B., Thurman, R.~E., John, S., Sandstrom, R., Johnson, A.~K., Maurano, M.~T.,
Humbert, R., Rynes, E., Wang, H., Vong, S., Lee, K., Bates, D., Diegel, M.,
Roach, V., Dunn, D., Neri, J., Schafer, A., Hansen, R.~S., Kutyavin, T.,
Giste, E., Weaver, M., Canfield, T., Sabo, P., Zhang, M., Balasundaram, G.,
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R., and Stamatoyannopoulos, J.~A. (2012).
\newblock An expansive human regulatory lexicon encoded in transcription factor
footprints.
\newblock {\em Nature}, 489(7414):83--90.
\bibitem[Nielsen et~al., 2012]{nielsen_catchprofiles:_2012}
Nielsen, F. G.~G., Markus, K.~G., Friborg, R.~M., Favrholdt, L.~M.,
Stunnenberg, H.~G., and Huynen, M. (2012).
\newblock {CATCHprofiles}: {Clustering} and {Alignment} {Tool} for {ChIP}
{Profiles}.
\newblock {\em PLOS ONE}, 7(1):e28272.
\bibitem[Orenstein and Shamir, 2014]{orenstein_comparative_2014}
Orenstein, Y. and Shamir, R. (2014).
\newblock A comparative analysis of transcription factor binding models learned
from {PBM}, {HT}-{SELEX} and {ChIP} data.
\newblock {\em Nucleic Acids Research}, 42(8):e63--e63.
\bibitem[Ou et~al., 2018]{ou_motifstack_2018}
Ou, J., Wolfe, S.~A., Brodsky, M.~H., and Zhu, L.~J. (2018).
\newblock {motifStack} for the analysis of transcription factor binding site
evolution.
\newblock {\em Nature Methods}, 15(1):8--9.
\bibitem[Soufi et~al., 2015]{soufi_pioneer_2015}
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Zaret, K.~S. (2015).
\newblock Pioneer {Transcription} {Factors} {Target} {Partial} {DNA} {Motifs}
on {Nucleosomes} to {Initiate} {Reprogramming}.
\newblock {\em Cell}, 161(3):555--568.
\bibitem[Vierstra and Stamatoyannopoulos, 2016]{vierstra_genomic_2016}
Vierstra, J. and Stamatoyannopoulos, J.~A. (2016).
\newblock Genomic footprinting.
\newblock {\em Nature Methods}, 13(3):213--221.
\bibitem[Voss and Hager, 2014]{voss_dynamic_2014}
Voss, T.~C. and Hager, G.~L. (2014).
\newblock Dynamic regulation of transcriptional states by chromatin and
transcription factors.
\newblock {\em Nature Reviews Genetics}, 15(2):69--81.
\bibitem[Zaret and Carroll, 2011]{zaret_pioneer_2011}
Zaret, K.~S. and Carroll, J.~S. (2011).
\newblock Pioneer transcription factors: establishing competence for gene
expression.
\newblock {\em Genes \& Development}, 25(21):2227--2241.
\end{thebibliography}

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