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\begin{thebibliography}{}
\bibitem[Adey et~al., 2010]{adey_rapid_2010}
Adey, A., Morrison, H.~G., {Asan}, Xun, X., Kitzman, J.~O., Turner, E.~H.,
Stackhouse, B., MacKenzie, A.~P., Caruccio, N.~C., Zhang, X., and Shendure,
J. (2010).
\newblock Rapid, low-input, low-bias construction of shotgun fragment libraries
by high-density in vitro transposition.
\newblock {\em Genome Biology}, 11(12):R119.
\bibitem[Aerts et~al., 2003]{aerts_toucan:_2003}
Aerts, S., Thijs, G., Coessens, B., Staes, M., Moreau, Y., and Moor, B.~D.
(2003).
\newblock Toucan: deciphering the cis ‐regulatory logic of coregulated genes.
\newblock {\em Nucleic Acids Research}, 31(6):1753--1764.
\bibitem[Aibar et~al., 2017]{aibar_scenic:_2017}
Aibar, S., González-Blas, C.~B., Moerman, T., Huynh-Thu, V.~A., Imrichova, H.,
Hulselmans, G., Rambow, F., Marine, J.-C., Geurts, P., Aerts, J., van~den
Oord, J., Atak, Z.~K., Wouters, J., and Aerts, S. (2017).
\newblock {SCENIC}: single-cell regulatory network inference and clustering.
\newblock {\em Nature Methods}, 14(11):1083--1086.
\bibitem[Alipanahi et~al., 2015]{alipanahi_predicting_2015}
Alipanahi, B., Delong, A., Weirauch, M.~T., and Frey, B.~J. (2015).
\newblock Predicting the sequence specificities of {DNA}- and {RNA}-binding
proteins by deep learning.
\newblock {\em Nature Biotechnology}, 33(8):831--838.
\bibitem[Ambrosini et~al., 2016a]{ambrosini_chip-seq_2016}
Ambrosini, G., Dreos, R., Kumar, S., and Bucher, P. (2016a).
\newblock The {ChIP}-{Seq} tools and web server: a resource for analyzing
{ChIP}-seq and other types of genomic data.
\newblock {\em BMC Genomics}, 17:938.
\bibitem[Ambrosini et~al., 2016b]{ambrosini_chip-seq_2016-1}
Ambrosini, G., Dreos, R., Kumar, S., and Bucher, P. (2016b).
\newblock The {ChIP}-{Seq} tools and web server: a resource for analyzing
{ChIP}-seq and other types of genomic data.
\newblock {\em BMC Genomics}, 17(1):938.
\bibitem[Ambrosini et~al., 2018]{ambrosini_pwmscan:_2018}
Ambrosini, G., Groux, R., and Bucher, P. (2018).
\newblock {PWMScan}: a fast tool for scanning entire genomes with a
position-specific weight matrix.
\newblock {\em Bioinformatics}, 34(14):2483--2484.
\bibitem[Ambrosini et~al., 2003]{ambrosini_signal_2003}
Ambrosini, G., Praz, V., Jagannathan, V., and Bucher, P. (2003).
\newblock Signal search analysis server.
\newblock {\em Nucleic Acids Research}, 31(13):3618--3620.
\bibitem[Angerer et~al., 2017]{angerer_single_2017}
Angerer, P., Simon, L., Tritschler, S., Wolf, F.~A., Fischer, D., and Theis,
F.~J. (2017).
\newblock Single cells make big data: {New} challenges and opportunities in
transcriptomics.
\newblock {\em Current Opinion in Systems Biology}, 4:85--91.
\bibitem[Bailey et~al., 2015]{bailey_znf143_2015}
Bailey, S.~D., Zhang, X., Desai, K., Aid, M., Corradin, O., Cowper-Sal·lari,
R., Akhtar-Zaidi, B., Scacheri, P.~C., Haibe-Kains, B., and Lupien, M.
(2015).
\newblock {ZNF}143 provides sequence specificity to secure chromatin
interactions at gene promoters.
\newblock {\em Nature Communications}, 2:6186.
\bibitem[Bailey et~al., 2009]{bailey_meme_2009}
Bailey, T.~L., Boden, M., Buske, F.~A., Frith, M., Grant, C.~E., Clementi, L.,
Ren, J., Li, W.~W., and Noble, W.~S. (2009).
\newblock {MEME} {Suite}: tools for motif discovery and searching.
\newblock {\em Nucleic Acids Research}, 37(suppl\_2):W202--W208.
\bibitem[Barrett et~al., 2011]{barrett_ncbi_2011}
Barrett, T., Troup, D.~B., Wilhite, S.~E., Ledoux, P., Evangelista, C., Kim,
I.~F., Tomashevsky, M., Marshall, K.~A., Phillippy, K.~H., Sherman, P.~M.,
Muertter, R.~N., Holko, M., Ayanbule, O., Yefanov, A., and Soboleva, A.
(2011).
\newblock {NCBI} {GEO}: archive for functional genomics data sets—10 years
on.
\newblock {\em Nucleic Acids Research}, 39(suppl\_1):D1005--D1010.
\bibitem[Barski et~al., 2007]{barski_high-resolution_2007}
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D.~E., Wang, Z., Wei,
G., Chepelev, I., and Zhao, K. (2007).
\newblock High-{Resolution} {Profiling} of {Histone} {Methylations} in the
{Human} {Genome}.
\newblock {\em Cell}, 129(4):823--837.
\bibitem[Beckstette et~al., 2006]{beckstette_fast_2006}
Beckstette, M., Homann, R., Giegerich, R., and Kurtz, S. (2006).
\newblock Fast index based algorithms and software for matching position
specific scoring matrices.
\newblock {\em BMC Bioinformatics}, 7:389.
\bibitem[Berest et~al., 2018]{berest_quantification_2018}
Berest, I., Arnold, C., Reyes-Palomares, A., Palla, G., Rasmussen, K.~D.,
Helin, K., and Zaugg, J. (2018).
\newblock Quantification of differential transcription factor activity and
multiomics-based classification into activators and repressors: {diffTF}.
\newblock {\em bioRxiv}.
\bibitem[Berger and Bulyk, 2009]{berger_universal_2009}
Berger, M.~F. and Bulyk, M.~L. (2009).
\newblock Universal protein-binding microarrays for the comprehensive
characterization of the {DNA}-binding specificities of transcription factors.
\newblock {\em Nature Protocols}, 4(3):393--411.
\bibitem[Boller et~al., 2018]{boller_defining_2018}
Boller, S., Li, R., and Grosschedl, R. (2018).
\newblock Defining {B} {Cell} {Chromatin}: {Lessons} from {EBF}1.
\newblock {\em Trends in Genetics}, 34(4):257--269.
\bibitem[Boller et~al., 2016]{boller_pioneering_2016}
Boller, S., Ramamoorthy, S., Akbas, D., Nechanitzky, R., Burger, L., Murr, R.,
Schübeler, D., and Grosschedl, R. (2016).
\newblock Pioneering {Activity} of the {C}-{Terminal} {Domain} of {EBF}1
{Shapes} the {Chromatin} {Landscape} for {B} {Cell} {Programming}.
\newblock {\em Immunity}, 44(3):527--541.
\bibitem[Boyle et~al., 2008]{boyle_high-resolution_2008}
Boyle, A.~P., Davis, S., Shulha, H.~P., Meltzer, P., Margulies, E.~H., Weng,
Z., Furey, T.~S., and Crawford, G.~E. (2008).
\newblock High-{Resolution} {Mapping} and {Characterization} of {Open}
{Chromatin} across the {Genome}.
\newblock {\em Cell}, 132(2):311--322.
\bibitem[Bucher and Trifonov, 1986]{bucher_compilation_1986}
Bucher, P. and Trifonov, E.~N. (1986).
\newblock Compilation and analysis of eukaryotic {POL} {II} promoter sequences.
\newblock {\em Nucleic Acids Research}, 14(24):10009--10026.
\bibitem[Buenrostro et~al., 2013]{buenrostro_transposition_2013}
Buenrostro, J.~D., Giresi, P.~G., Zaba, L.~C., Chang, H.~Y., and Greenleaf,
W.~J. (2013).
\newblock Transposition of native chromatin for fast and sensitive epigenomic
profiling of open chromatin, {DNA}-binding proteins and nucleosome position.
\newblock {\em Nature Methods}, 10(12):1213--1218.
\bibitem[Castro-Mondragon et~al., 2017]{castro-mondragon_rsat_2017}
Castro-Mondragon, J.~A., Jaeger, S., Thieffry, D., Thomas-Chollier, M., and van
Helden, J. (2017).
\newblock {RSAT} matrix-clustering: dynamic exploration and redundancy
reduction of transcription factor binding motif collections.
\newblock {\em Nucleic Acids Research}, 45(13):e119--e119.
\bibitem[Chatr-aryamontri et~al., 2017]{chatr-aryamontri_biogrid_2017}
Chatr-aryamontri, A., Oughtred, R., Boucher, L., Rust, J., Chang, C., Kolas,
N.~K., O'Donnell, L., Oster, S., Theesfeld, C., Sellam, A., Stark, C.,
Breitkreutz, B.-J., Dolinski, K., and Tyers, M. (2017).
\newblock The {BioGRID} interaction database: 2017 update.
\newblock {\em Nucleic Acids Research}, 45(D1):D369--D379.
\bibitem[Cheng et~al., 2012]{cheng_understanding_2012}
Cheng, C., Alexander, R., Min, R., Leng, J., Yip, K.~Y., Rozowsky, J., Yan,
K.-K., Dong, X., Djebali, S., Ruan, Y., Davis, C.~A., Carninci, P., Lassman,
T., Gingeras, T.~R., Guigó, R., Birney, E., Weng, Z., Snyder, M., and
Gerstein, M. (2012).
\newblock Understanding transcriptional regulation by integrative analysis of
transcription factor binding data.
\newblock {\em Genome Research}, 22(9):1658--1667.
\bibitem[Cirillo et~al., 2002]{cirillo_opening_2002}
Cirillo, L.~A., Lin, F.~R., Cuesta, I., Friedman, D., Jarnik, M., and Zaret,
K.~S. (2002).
\newblock Opening of {Compacted} {Chromatin} by {Early} {Developmental}
{Transcription} {Factors} {HNF}3 ({FoxA}) and {GATA}-4.
\newblock {\em Molecular Cell}, 9(2):279--289.
\bibitem[Consortium, 2012]{consortium_integrated_2012}
Consortium, T. E.~P. (2012).
\newblock An integrated encyclopedia of {DNA} elements in the human genome.
\newblock {\em Nature}, 489(7414):57--74.
\bibitem[Donohoe et~al., 2007]{donohoe_identification_2007}
Donohoe, M.~E., Zhang, L.-F., Xu, N., Shi, Y., and Lee, J.~T. (2007).
\newblock Identification of a {Ctcf} {Cofactor}, {Yy}1, for the {X}
{Chromosome} {Binary} {Switch}.
\newblock {\em Molecular Cell}, 25(1):43--56.
\bibitem[Dreos et~al., 2013]{dreos_epd_2013}
Dreos, R., Ambrosini, G., Cavin~Périer, R., and Bucher, P. (2013).
\newblock {EPD} and {EPDnew}, high-quality promoter resources in the
next-generation sequencing era.
\newblock {\em Nucleic Acids Research}, 41(D1):D157--D164.
\bibitem[Dreos et~al., 2017]{dreos_eukaryotic_2017}
Dreos, R., Ambrosini, G., Groux, R., Cavin Périer, R., and Bucher, P. (2017).
\newblock The eukaryotic promoter database in its 30th year: focus on
non-vertebrate organisms.
\newblock {\em Nucleic Acids Research}, 45(D1):D51--D55.
\bibitem[Dreos et~al., 2018]{dreos_mga_2018}
Dreos, R., Ambrosini, G., Groux, R., Périer, R.~C., and Bucher, P. (2018).
\newblock {MGA} repository: a curated data resource for {ChIP}-seq and other
genome annotated data.
\newblock {\em Nucleic Acids Research}, 46(D1):D175--D180.
\bibitem[Dreos et~al., 2015]{dreos_eukaryotic_2015}
Dreos, R., Ambrosini, G., Périer, R.~C., and Bucher, P. (2015).
\newblock The {Eukaryotic} {Promoter} {Database}: expansion of {EPDnew} and new
promoter analysis tools.
\newblock {\em Nucleic Acids Research}, 43(D1):D92--D96.
\bibitem[Fan et~al., 2016]{fan_characterizing_2016}
Fan, J., Salathia, N., Liu, R., Kaeser, G.~E., Yung, Y.~C., Herman, J.~L.,
Kaper, F., Fan, J.-B., Zhang, K., Chun, J., and Kharchenko, P.~V. (2016).
\newblock Characterizing transcriptional heterogeneity through pathway and gene
set overdispersion analysis.
\newblock {\em Nature Methods}, 13(3):241--244.
\bibitem[Fu et~al., 2004]{fu_motifviz:_2004}
Fu, Y., Frith, M.~C., Haverty, P.~M., and Weng, Z. (2004).
\newblock {MotifViz}: an analysis and visualization tool for motif discovery.
\newblock {\em Nucleic Acids Research}, 32(suppl\_2):W420--W423.
\bibitem[Fu et~al., 2008]{fu_insulator_2008}
Fu, Y., Sinha, M., Peterson, C.~L., and Weng, Z. (2008).
\newblock The {Insulator} {Binding} {Protein} {CTCF} {Positions} 20
{Nucleosomes} around {Its} {Binding} {Sites} across the {Human} {Genome}.
\newblock {\em PLOS Genetics}, 4(7):e1000138.
\bibitem[Gaffney et~al., 2012]{gaffney_controls_2012}
Gaffney, D.~J., McVicker, G., Pai, A.~A., Fondufe-Mittendorf, Y.~N., Lewellen,
N., Michelini, K., Widom, J., Gilad, Y., and Pritchard, J.~K. (2012).
\newblock Controls of {Nucleosome} {Positioning} in the {Human} {Genome}.
\newblock {\em PLoS Genet}, 8(11):e1003036.
\bibitem[Gerstein et~al., 2012]{gerstein_architecture_2012}
Gerstein, M.~B., Kundaje, A., Hariharan, M., Landt, S.~G., Yan, K.-K., Cheng,
C., Mu, X.~J., Khurana, E., Rozowsky, J., Alexander, R., Min, R., Alves, P.,
Abyzov, A., Addleman, N., Bhardwaj, N., Boyle, A.~P., Cayting, P., Charos,
A., Chen, D.~Z., Cheng, Y., Clarke, D., Eastman, C., Euskirchen, G., Frietze,
S., Fu, Y., Gertz, J., Grubert, F., Harmanci, A., Jain, P., Kasowski, M.,
Lacroute, P., Leng, J., Lian, J., Monahan, H., O’Geen, H., Ouyang, Z.,
Partridge, E.~C., Patacsil, D., Pauli, F., Raha, D., Ramirez, L., Reddy,
T.~E., Reed, B., Shi, M., Slifer, T., Wang, J., Wu, L., Yang, X., Yip, K.~Y.,
Zilberman-Schapira, G., Batzoglou, S., Sidow, A., Farnham, P.~J., Myers,
R.~M., Weissman, S.~M., and Snyder, M. (2012).
\newblock Architecture of the human regulatory network derived from {ENCODE}
data.
\newblock {\em Nature}, 489(7414):91--100.
\bibitem[Ghirlando and Felsenfeld, 2016]{ghirlando_ctcf:_2016}
Ghirlando, R. and Felsenfeld, G. (2016).
\newblock {CTCF}: making the right connections.
\newblock {\em Genes \& Development}, 30(8):881--891.
\bibitem[González-Blas et~al., 2019]{gonzalez-blas_cistopic:_2019}
González-Blas, C.~B., Minnoye, L., Papasokrati, D., Aibar, S., Hulselmans, G.,
Christiaens, V., Davie, K., Wouters, J., and Aerts, S. (2019).
\newblock {cisTopic}: cis-regulatory topic modeling on single-cell {ATAC}-seq
data.
\newblock {\em Nature Methods}, 16(5):397.
\bibitem[Grant et~al., 2011]{grant_fimo:_2011}
Grant, C.~E., Bailey, T.~L., and Noble, W.~S. (2011).
\newblock {FIMO}: scanning for occurrences of a given motif.
\newblock {\em Bioinformatics}, 27(7):1017--1018.
\bibitem[Grossman et~al., 2018]{grossman_positional_2018}
Grossman, S.~R., Engreitz, J., Ray, J.~P., Nguyen, T.~H., Hacohen, N., and
Lander, E.~S. (2018).
\newblock Positional specificity of different transcription factor classes
within enhancers.
\newblock {\em Proceedings of the National Academy of Sciences},
115(30):E7222--E7230.
\bibitem[Groux and Bucher, 2019]{groux_spar-k:_2019}
Groux, R. and Bucher, P. (2019).
\newblock {SPar}-{K}: a method to partition {NGS} signal data.
\newblock {\em Bioinformatics}.
\bibitem[Guo et~al., 2012]{guo_high_2012}
Guo, Y., Mahony, S., and Gifford, D.~K. (2012).
\newblock High {Resolution} {Genome} {Wide} {Binding} {Event} {Finding} and
{Motif} {Discovery} {Reveals} {Transcription} {Factor} {Spatial} {Binding}
{Constraints}.
\newblock {\em PLOS Computational Biology}, 8(8):e1002638.
\bibitem[Hagman and Lukin, 2005]{hagman_early_2005}
Hagman, J. and Lukin, K. (2005).
\newblock Early {B}-cell factor ‘pioneers’ the way for {B}-cell
development.
\newblock {\em Trends in Immunology}, 26(9):455--461.
\bibitem[Heinz et~al., 2010]{heinz_simple_2010}
Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y.~C., Laslo, P., Cheng,
J.~X., Murre, C., Singh, H., and Glass, C.~K. (2010).
\newblock Simple {Combinations} of {Lineage}-{Determining} {Transcription}
{Factors} {Prime} cis-{Regulatory} {Elements} {Required} for {Macrophage} and
{B} {Cell} {Identities}.
\newblock {\em Molecular Cell}, 38(4):576--589.
\bibitem[Hepler, 2018]{hepler_10x_2018}
Hepler, L. (2018).
\newblock 10x {Genomics} takes gene imaging and analysis tools to the big
leagues.
\bibitem[Hertz et~al., 1990]{hertz_identification_1990}
Hertz, G.~Z., Hartzell, G.~W., and Stormo, G.~D. (1990).
\newblock Identification of consensus patterns in unaligned {DNA} sequences
known to be functionally related.
\newblock {\em Computer applications in the biosciences: CABIOS}, 6(2):81--92.
\bibitem[Hon et~al., 2008]{hon_chromasig:_2008}
Hon, G., Ren, B., and Wang, W. (2008).
\newblock {ChromaSig}: {A} {Probabilistic} {Approach} to {Finding} {Common}
{Chromatin} {Signatures} in the {Human} {Genome}.
\newblock {\em PLOS Computational Biology}, 4(10):e1000201.
\bibitem[Ioshikhes et~al., 2011]{ioshikhes_variety_2011}
Ioshikhes, I., Hosid, S., and Pugh, B.~F. (2011).
\newblock Variety of genomic {DNA} patterns for nucleosome positioning.
\newblock {\em Genome Research}, 21(11):1863--1871.
\bibitem[Isakova et~al., 2017]{isakova_smile-seq_2017}
Isakova, A., Groux, R., Imbeault, M., Rainer, P., Alpern, D., Dainese, R.,
Ambrosini, G., Trono, D., Bucher, P., and Deplancke, B. (2017).
\newblock {SMiLE}-seq identifies binding motifs of single and dimeric
transcription factors.
\newblock {\em Nature Methods}, advance online publication.
\bibitem[Jolma et~al., 2010]{jolma_multiplexed_2010}
Jolma, A., Kivioja, T., Toivonen, J., Cheng, L., Wei, G., Enge, M., Taipale,
M., Vaquerizas, J.~M., Yan, J., Sillanpää, M.~J., Bonke, M., Palin, K.,
Talukder, S., Hughes, T.~R., Luscombe, N.~M., Ukkonen, E., and Taipale, J.
(2010).
\newblock Multiplexed massively parallel {SELEX} for characterization of human
transcription factor binding specificities.
\newblock {\em Genome Research}, 20(6):861--873.
\bibitem[Jolma et~al., 2013]{jolma_dna-binding_2013}
Jolma, A., Yan, J., Whitington, T., Toivonen, J., Nitta, K., Rastas, P.,
Morgunova, E., Enge, M., Taipale, M., Wei, G., Palin, K., Vaquerizas, J.,
Vincentelli, R., Luscombe, N., Hughes, T., Lemaire, P., Ukkonen, E., Kivioja,
T., and Taipale, J. (2013).
\newblock {DNA}-{Binding} {Specificities} of {Human} {Transcription} {Factors}.
\newblock {\em Cell}, 152(1–2):327--339.
\bibitem[Kent, 2002]{kent_blatblast-like_2002}
Kent, W.~J. (2002).
\newblock {BLAT}—{The} {BLAST}-{Like} {Alignment} {Tool}.
\newblock {\em Genome Research}, 12(4):656--664.
\bibitem[Khan et~al., 2018]{khan_jaspar_2018}
Khan, A., Fornes, O., Stigliani, A., Gheorghe, M., Castro-Mondragon, J.~A., van
der Lee, R., Bessy, A., Chèneby, J., Kulkarni, S.~R., Tan, G., Baranasic,
D., Arenillas, D.~J., Sandelin, A., Vandepoele, K., Lenhard, B., Ballester,
B., Wasserman, W.~W., Parcy, F., and Mathelier, A. (2018).
\newblock {JASPAR} 2018: update of the open-access database of transcription
factor binding profiles and its web framework.
\newblock {\em Nucleic Acids Research}, 46(D1):D260--D266.
\bibitem[Kiselev et~al., 2017]{kiselev_sc3:_2017}
Kiselev, V.~Y., Kirschner, K., Schaub, M.~T., Andrews, T., Yiu, A., Chandra,
T., Natarajan, K.~N., Reik, W., Barahona, M., Green, A.~R., and Hemberg, M.
(2017).
\newblock {SC}3: consensus clustering of single-cell {RNA}-seq data.
\newblock {\em Nature Methods}, 14(5):483--486.
\bibitem[Kulakovskiy et~al., 2018]{kulakovskiy_hocomoco:_2018}
Kulakovskiy, I.~V., Vorontsov, I.~E., Yevshin, I.~S., Sharipov, R.~N.,
Fedorova, A.~D., Rumynskiy, E.~I., Medvedeva, Y.~A., Magana-Mora, A., Bajic,
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.
\newblock {\em Nucleic Acids Research}, 46(D1):D252--D259.
\bibitem[Kulakovskiy et~al., 2016]{kulakovskiy_hocomoco:_2016}
Kulakovskiy, I.~V., Vorontsov, I.~E., Yevshin, I.~S., Soboleva, A.~V.,
Kasianov, A.~S., Ashoor, H., Ba-alawi, W., Bajic, V.~B., Medvedeva, Y.~A.,
Kolpakov, F.~A., and Makeev, V.~J. (2016).
\newblock {HOCOMOCO}: expansion and enhancement of the collection of
transcription factor binding sites models.
\newblock {\em Nucleic Acids Research}, 44(D1):D116--D125.
\bibitem[Kundaje et~al., 2012]{kundaje_ubiquitous_2012}
Kundaje, A., Kyriazopoulou-Panagiotopoulou, S., Libbrecht, M., Smith, C.~L.,
Raha, D., Winters, E.~E., Johnson, S.~M., Snyder, M., Batzoglou, S., and
Sidow, A. (2012).
\newblock Ubiquitous heterogeneity and asymmetry of the chromatin environment
at regulatory elements.
\newblock {\em Genome Research}, 22(9):1735--1747.
\bibitem[Langmead and Salzberg, 2012]{langmead_fast_2012}
Langmead, B. and Salzberg, S.~L. (2012).
\newblock Fast gapped-read alignment with {Bowtie} 2.
\newblock {\em Nature Methods}, 9(4):357--359.
\bibitem[Langmead et~al., 2009]{langmead_ultrafast_2009}
Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.~L. (2009).
\newblock Ultrafast and memory-efficient alignment of short {DNA} sequences to
the human genome.
\newblock {\em Genome Biology}, 10(3):R25.
\bibitem[Li et~al., 2009]{li_sequence_2009}
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth,
G., Abecasis, G., and Durbin, R. (2009).
\newblock The {Sequence} {Alignment}/{Map} format and {SAMtools}.
\newblock {\em Bioinformatics}, 25(16):2078--2079.
\bibitem[Li et~al., 2019]{li_identification_2019}
Li, Z., Schulz, M.~H., Look, T., Begemann, M., Zenke, M., and Costa, I.~G.
(2019).
\newblock Identification of transcription factor binding sites using
{ATAC}-seq.
\newblock {\em Genome Biology}, 20(1):45.
\bibitem[Lizio et~al., 2015]{lizio_gateways_2015}
Lizio, M., Harshbarger, J., Shimoji, H., Severin, J., Kasukawa, T., Sahin, S.,
Abugessaisa, I., Fukuda, S., Hori, F., Ishikawa-Kato, S., Mungall, C.~J.,
Arner, E., Baillie, J.~K., Bertin, N., Bono, H., de~Hoon, M., Diehl, A.~D.,
Dimont, E., Freeman, T.~C., Fujieda, K., Hide, W., Kaliyaperumal, R.,
Katayama, T., Lassmann, T., Meehan, T.~F., Nishikata, K., Ono, H., Rehli, M.,
Sandelin, A., Schultes, E.~A., ‘t Hoen, P.~A., Tatum, Z., Thompson, M.,
Toyoda, T., Wright, D.~W., Daub, C.~O., Itoh, M., Carninci, P., Hayashizaki,
Y., Forrest, A.~R., Kawaji, H., and {the FANTOM consortium} (2015).
\newblock Gateways to the {FANTOM}5 promoter level mammalian expression atlas.
\newblock {\em Genome Biology}, 16(1):22.
\bibitem[Losada, 2014]{losada_cohesin_2014}
Losada, A. (2014).
\newblock Cohesin in cancer: chromosome segregation and beyond.
\newblock {\em Nature Reviews Cancer}, 14(6):389--393.
\bibitem[Maerkl and Quake, 2007]{maerkl_systems_2007}
Maerkl, S.~J. and Quake, S.~R. (2007).
\newblock A {Systems} {Approach} to {Measuring} the {Binding} {Energy}
{Landscapes} of {Transcription} {Factors}.
\newblock {\em Science}, 315(5809):233--237.
\bibitem[Maier et~al., 2004]{maier_early_2004}
Maier, H., Ostraat, R., Gao, H., Fields, S., Shinton, S.~A., Medina, K.~L.,
Ikawa, T., Murre, C., Singh, H., Hardy, R.~R., and Hagman, J. (2004).
\newblock Early {B} cell factor cooperates with {Runx}1 and mediates epigenetic
changes associated with mb-1 transcription.
\newblock {\em Nature Immunology}, 5(10):1069--1077.
\bibitem[Mathelier et~al., 2014]{mathelier_jaspar_2014}
Mathelier, A., Zhao, X., Zhang, A.~W., Parcy, F., Worsley-Hunt, R., Arenillas,
D.~J., Buchman, S., Chen, C.-y., Chou, A., Ienasescu, H., Lim, J., Shyr, C.,
Tan, G., Zhou, M., Lenhard, B., Sandelin, A., and Wasserman, W.~W. (2014).
\newblock {JASPAR} 2014: an extensively expanded and updated open-access
database of transcription factor binding profiles.
\newblock {\em Nucleic Acids Research}, 42(D1):D142--D147.
\bibitem[Nair et~al., 2014]{nair_probabilistic_2014}
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.,
Byron, R., MacCoss, M.~J., Akey, J.~M., Bender, M.~A., Groudine, M., Kaul,
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[Ong and Corces, 2014]{ong_ctcf:_2014}
Ong, C.-T. and Corces, V.~G. (2014).
\newblock {CTCF}: an architectural protein bridging genome topology and
function.
\newblock {\em Nature Reviews Genetics}, 15(4):234--246.
\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[Pizzi and Ukkonen, 2008]{pizzi_fast_2008}
Pizzi, C. and Ukkonen, E. (2008).
\newblock Fast profile matching algorithms — {A} survey.
\newblock {\em Theoretical Computer Science}, 395(2):137--157.
\bibitem[Pollard et~al., 2010]{pollard_detection_2010}
Pollard, K.~S., Hubisz, M.~J., Rosenbloom, K.~R., and Siepel, A. (2010).
\newblock Detection of nonneutral substitution rates on mammalian phylogenies.
\newblock {\em Genome Research}, 20(1):110--121.
\bibitem[Quinlan and Hall, 2010]{quinlan_bedtools:_2010}
Quinlan, A.~R. and Hall, I.~M. (2010).
\newblock {BEDTools}: a flexible suite of utilities for comparing genomic
features.
\newblock {\em Bioinformatics}, 26(6):841--842.
\bibitem[Raney et~al., 2014]{raney_track_2014}
Raney, B.~J., Dreszer, T.~R., Barber, G.~P., Clawson, H., Fujita, P.~A., Wang,
T., Nguyen, N., Paten, B., Zweig, A.~S., Karolchik, D., and Kent, W.~J.
(2014).
\newblock Track data hubs enable visualization of user-defined genome-wide
annotations on the {UCSC} {Genome} {Browser}.
\newblock {\em Bioinformatics}, 30(7):1003--1005.
\bibitem[{Roadmap Epigenomics Consortium} et~al.,
2015]{roadmap_epigenomics_consortium_integrative_2015}
{Roadmap Epigenomics Consortium}, Kundaje, A., Meuleman, W., Ernst, J.,
Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang,
J., Ziller, M.~J., Amin, V., Whitaker, J.~W., Schultz, M.~D., Ward, L.~D.,
Sarkar, A., Quon, G., Sandstrom, R.~S., Eaton, M.~L., Wu, Y.-C., Pfenning,
A.~R., Wang, X., Claussnitzer, M., {Yaping Liu}, Coarfa, C., Alan~Harris, R.,
Shoresh, N., Epstein, C.~B., Gjoneska, E., Leung, D., Xie, W., David~Hawkins,
R., Lister, R., Hong, C., Gascard, P., Mungall, A.~J., Moore, R., Chuah, E.,
Tam, A., Canfield, T.~K., Scott~Hansen, R., Kaul, R., Sabo, P.~J., Bansal,
M.~S., Carles, A., Dixon, J.~R., Farh, K.-H., Feizi, S., Karlic, R., Kim,
A.-R., Kulkarni, A., Li, D., Lowdon, R., Elliott, G., Mercer, T.~R., Neph,
S.~J., Onuchic, V., Polak, P., Rajagopal, N., Ray, P., Sallari, R.~C.,
Siebenthall, K.~T., Sinnott-Armstrong, N.~A., Stevens, M., Thurman, R.~E.,
Wu, J., Zhang, B., Zhou, X., Beaudet, A.~E., Boyer, L.~A., Jager, P. L.~D.,
Farnham, P.~J., Fisher, S.~J., Haussler, D., Jones, S. J.~M., Li, W., Marra,
M.~A., McManus, M.~T., Sunyaev, S., Thomson, J.~A., Tlsty, T.~D., Tsai,
L.-H., Wang, W., Waterland, R.~A., Zhang, M.~Q., Chadwick, L.~H., Bernstein,
B.~E., Costello, J.~F., Ecker, J.~R., Hirst, M., Meissner, A., Milosavljevic,
A., Ren, B., Stamatoyannopoulos, J.~A., Wang, T., and Kellis, M. (2015).
\newblock Integrative analysis of 111 reference human epigenomes.
\newblock {\em Nature}, 518(7539):317--330.
\bibitem[Rustici et~al., 2013]{rustici_arrayexpress_2013}
Rustici, G., Kolesnikov, N., Brandizi, M., Burdett, T., Dylag, M., Emam, I.,
Farne, A., Hastings, E., Ison, J., Keays, M., Kurbatova, N., Malone, J.,
Mani, R., Mupo, A., Pedro~Pereira, R., Pilicheva, E., Rung, J., Sharma, A.,
Tang, Y.~A., Ternent, T., Tikhonov, A., Welter, D., Williams, E., Brazma, A.,
Parkinson, H., and Sarkans, U. (2013).
\newblock {ArrayExpress} update—trends in database growth and links to data
analysis tools.
\newblock {\em Nucleic Acids Research}, 41(D1):D987--D990.
\bibitem[Schones et~al., 2007]{schones_statistical_2007}
Schones, D.~E., Smith, A.~D., and Zhang, M.~Q. (2007).
\newblock Statistical significance of cis-regulatory modules.
\newblock {\em BMC Bioinformatics}, 8(1):19.
\bibitem[Schütz and Delorenzi, 2008]{schutz_mamot:_2008}
Schütz, F. and Delorenzi, M. (2008).
\newblock {MAMOT}: hidden {Markov} modeling tool.
\newblock {\em Bioinformatics}, 24(11):1399--1400.
\bibitem[Siepel et~al., 2005]{siepel_evolutionarily_2005}
Siepel, A., Bejerano, G., Pedersen, J.~S., Hinrichs, A.~S., Hou, M.,
Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.~W., Richards, S.,
Weinstock, G.~M., Wilson, R.~K., Gibbs, R.~A., Kent, W.~J., Miller, W., and
Haussler, D. (2005).
\newblock Evolutionarily conserved elements in vertebrate, insect, worm, and
yeast genomes.
\newblock {\em Genome Research}, 15(8):1034--1050.
\bibitem[Soufi et~al., 2015]{soufi_pioneer_2015}
Soufi, A., Garcia, M.~F., Jaroszewicz, A., Osman, N., Pellegrini, M., and
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[Stedman et~al., 2008]{stedman_cohesins_2008}
Stedman, W., Kang, H., Lin, S., Kissil, J.~L., Bartolomei, M.~S., and
Lieberman, P.~M. (2008).
\newblock Cohesins localize with {CTCF} at the {KSHV} latency control region
and at cellular c-myc and {H}19 {Igf}2 insulators.
\newblock {\em The EMBO Journal}, 27(4):654--666.
\bibitem[Trifonov, 2011]{trifonov_cracking_2011}
Trifonov, E.~N. (2011).
\newblock Cracking the chromatin code: {Precise} rule of nucleosome
positioning.
\newblock {\em Physics of Life Reviews}, 8(1):39--50.
\bibitem[Turatsinze et~al., 2008]{turatsinze_using_2008}
Turatsinze, J.-V., Thomas-Chollier, M., Defrance, M., and Helden, J.~v. (2008).
\newblock Using {RSAT} to scan genome sequences for transcription factor
binding sites and cis -regulatory modules.
\newblock {\em Nature Protocols}, 3(10):1578--1588.
\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[Wang et~al., 2012]{wang_sequence_2012}
Wang, J., Zhuang, J., Iyer, S., Lin, X., Whitfield, T.~W., Greven, M.~C.,
Pierce, B.~G., Dong, X., Kundaje, A., Cheng, Y., Rando, O.~J., Birney, E.,
Myers, R.~M., Noble, W.~S., Snyder, M., and Weng, Z. (2012).
\newblock Sequence features and chromatin structure around the genomic regions
bound by 119 human transcription factors.
\newblock {\em Genome Research}, 22(9):1798--1812.
\bibitem[Weirauch et~al., 2013]{weirauch_evaluation_2013}
Weirauch, M.~T., Cote, A., Norel, R., Annala, M., Zhao, Y., Riley, T.~R.,
Saez-Rodriguez, J., Cokelaer, T., Vedenko, A., Talukder, S., {Dream5
Consortium}, Bussemaker, H.~J., Morris, Q.~D., Bulyk, M.~L., Stolovitzky, G.,
and Hughes, T.~R. (2013).
\newblock Evaluation of methods for modeling transcription factor sequence
specificity.
\newblock {\em Nature Biotechnology}, 31(2):126--134.
\bibitem[Wu et~al., 2016]{wu_biogps:_2016}
Wu, C., Jin, X., Tsueng, G., Afrasiabi, C., and Su, A.~I. (2016).
\newblock {BioGPS}: building your own mash-up of gene annotations and
expression profiles.
\newblock {\em Nucleic Acids Research}, 44(D1):D313--D316.
\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.
\bibitem[Zhang et~al., 2014]{zhang_canonical_2014}
Zhang, Y., Vastenhouw, N.~L., Feng, J., Fu, K., Wang, C., Ge, Y., Pauli, A.,
Hummelen, P.~v., Schier, A.~F., and Liu, X.~S. (2014).
\newblock Canonical nucleosome organization at promoters forms during genome
activation.
\newblock {\em Genome Research}, 24(2):260--266.
\bibitem[Zhao et~al., 2005]{zhao_tred:_2005}
Zhao, F., Xuan, Z., Liu, L., and Zhang, M.~Q. (2005).
\newblock {TRED}: a {Transcriptional} {Regulatory} {Element} {Database} and a
platform for in silico gene regulation studies.
\newblock {\em Nucleic Acids Research}, 33(suppl\_1):D103--D107.
\bibitem[Zhao et~al., 2009]{zhao_inferring_2009}
Zhao, Y., Granas, D., and Stormo, G.~D. (2009).
\newblock Inferring {Binding} {Energies} from {Selected} {Binding} {Sites}.
\newblock {\em PLOS Comput Biol}, 5(12):e1000590.
\end{thebibliography}
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