@Article{LMRs,
  title   = {{DNA}-binding factors shape the mouse methylome at distal regulatory regions},
  author  = {Michael B. Stadler and Rabih Murr and Lukas Burger and Robert Ivanek and Florian Lienert and Anne Schöler and Erik van Nimwegen and Christiane Wirbelauer and Edward J. Oakeley and Dimos Gaidatzis and Vijay K. Tiwari and Dirk Schübeler},
  year    = {2011},
  journal = {Nature},
  volume  = {480},
  pages   = {490-495},
  doi     = {doi:10.1038/nature10716},
  url     = {https://www.nature.com/articles/nature10716}
}

@Article{MethylSeekR,
  title   = {Identification of active regulatory regions from {DNA} methylation data},
  author  = {Lukas Burger and Dimos Gaidatzis and Dirk Schuebeler and Michael B. Stadler},
  year    = {2013},
  journal = {Nucleic Acids Research},
  volume  = {41},
  pages   = {e155},
  doi     = {doi:10.1093/nar/gkt599},
  url     = {http://nar.oxfordjournals.org/content/41/16/e155.full}
}

@Article{Chromatome,
  title   = {Cell cycle-resolved chromatin proteomics reveals the extent of mitotic preservation of the genomic regulatory landscape},
  author  = {Paul A. Ginno and Lukas Burger and Jan Seebacher and Vytautas Iesmantavicius and Dirk Schuebler},
  year    = {2018},
  journal = {Nature Commun.},
  volume  = {9},
  pages   = {},
  doi     = {10.1038/s41467-018-06007-5},
  url     = {https://www.nature.com/articles/s41467-018-06007-5}
}

@Article{Snf2h,
  title   = {Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors},
  author  = {Darko Barisic and Michael B Stadler and Mario Iurlaro and Dirk Schuebler},
  year    = {2019},
  journal = {Nature},
  volume  = {569},
  pages   = {136-140},
  doi     = {10.1038/s41586-019-1115-5},
  url     = {https://www.nature.com/articles/s41586-019-1115-5}
}

@Article{StabSel,
  title   = {Stability selection},
  author  = {Meinshausen, Nicolai and B{\"{u}}hlmann, Peter},
  year    = {2010},
  month   = {jul},
  number  = {4},
  journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  volume  = {72},
  issn    = {13697412},
  pages   = {417--473},
  doi     = {doi:10.1111/j.1467-9868.2010.00740.x},
  url     = {http://doi.wiley.com/10.1111/j.1467-9868.2010.00740.x}
}

@Article{compStabs,
  title   = {Variable selection with error control: another look at stability selection},
  author  = {Shah, Rajen D. and Samworth, Richard J.},
  year    = {2013},
  month   = {jan},
  number  = {1},
  journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  volume  = {75},
  issn    = {13697412},
  pages   = {55--80},
  doi     = {doi:10.1111/j.1467-9868.2011.01034.x},
  url     = {http://doi.wiley.com/10.1111/j.1467-9868.2011.01034.x}
}

@Article{stabs,
  title   = {Controlling false discoveries in high-dimensional situations: Boosting with stability selection},
  author  = {Benjamin Hofner and Luigi Boccuto and Markus G\"oker},
  year    = {2015},
  journal = {BMC Bioinformatics},
  volume  = {16},
  pages   = {144},
  doi     = {doi:10.1186/s12859-015-0575-3},
  url     = {http://dx.doi.org/10.1186/s12859-015-0575-3}
}

@Article{QuasR,
  title   = {{QuasR}: quantification and annotation of short reads in R},
  author  = {Gaidatzis, Dimos and Lerch, Anita and Hahne, Florian and Stadler, Michael B.},
  year    = {2015},
  month   = {apr},
  number  = {7},
  journal = {Bioinformatics},
  volume  = {31},
  issn    = {1460-2059},
  pages   = {1130--1132},
  doi     = {doi:10.1093/bioinformatics/btu781},
  url     = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btu781}
}

@Article{encode,
  title   = {The Encyclopedia of {DNA} elements ({ENCODE}): data portal update},
  author  = {Davis, Carrie A and Hitz, Benjamin C and Sloan, Cricket A and Chan, Esther T and Davidson, Jean M and Gabdank, Idan and Hilton, Jason A and Jain, Kriti and Baymuradov, Ulugbek K and Narayanan, Aditi K and Onate, Kathrina C and Graham, Keenan and Miyasato, Stuart R and Dreszer, Timothy R and Strattan, J Seth and Jolanki, Otto and Tanaka, Forrest Y and Cherry, J Michael},
  year    = {2018},
  month   = {jan},
  number  = {D1},
  journal = {Nucleic Acids Research},
  volume  = {46},
  issn    = {0305-1048},
  pages   = {D794--D801},
  doi     = {doi:10.1093/nar/gkx1081},
  url     = {http://academic.oup.com/nar/article/46/D1/D794/4595865}
}

@Article{macs,
  title   = {Model-based analysis of ChIP-Seq ({MACS})},
  author  = {Zhang, Yong and Liu, Tao and Meyer, Clifford A and Eeckhoute, J{\'{e}}r{\^{o}}me and Johnson, David S and Bernstein, Bradley E and Nusbaum, Chad and Myers, Richard M and Brown, Myles and Li, Wei and Liu, X Shirley},
  year    = {2008},
  number  = {9},
  doi     = {10.1186/gb-2008-9-9-r137},
  journal = {Genome biology},
  volume  = {9},
  issn    = {1474-760X},
  pages   = {R137},
  pmid    = {18798982},
  doi     = {doi:10.1186/gb-2008-9-9-r137},
  url     = {http://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-9-r137}
}

@Article{reduce,
   Author="Roven, C.  and Bussemaker, H. J. ",
   Title="{{R}{E}{D}{U}{C}{E}: {A}n online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data}",
   Journal="Nucleic Acids Res",
   Year="2003",
   Volume="31",
   Number="13",
   Pages="3487--3490",
   Month="Jul"
}

@Article{ame,
   Author="McLeay, R. C.  and Bailey, T. L. ",
   Title="{{M}otif {E}nrichment {A}nalysis: a unified framework and an evaluation on {C}h{I}{P} data}",
   Journal="BMC Bioinformatics",
   Year="2010",
   Volume="11",
   Pages="165",
   Month="Apr"
}

@Article{ismara,
   Author="Balwierz, P. J.  and Pachkov, M.  and Arnold, P.  and Gruber, A. J.  and Zavolan, M.  and van Nimwegen, E. ",
   Title="{{I}{S}{M}{A}{R}{A}: automated modeling of genomic signals as a democracy of regulatory motifs}",
   Journal="Genome Res",
   Year="2014",
   Volume="24",
   Number="5",
   Pages="869--884",
   Month="May"
}

@Article{homer,
   Author="Heinz, S.  and Benner, C.  and Spann, N.  and Bertolino, E.  and Lin, Y. C.  and Laslo, P.  and Cheng, J. X.  and Murre, C.  and Singh, H.  and Glass, C. K. ",
   Title="{{S}imple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and {B} cell identities}",
   Journal="Mol Cell",
   Year="2010",
   Volume="38",
   Number="4",
   Pages="576--589",
   Month="May"
}

@Article{ginno2018,
   Author="Ginno, P. A.  and Burger, L.  and Seebacher, J.  and Iesmantavicius, V.  and Schübeler, D. ",
   Title="{{C}ell cycle-resolved chromatin proteomics reveals the extent of mitotic preservation of the genomic regulatory landscape}",
   Journal="Nat Commun",
   Year="2018",
   Volume="9",
   Number="1",
   Pages="4048",
   Month="10"
}

@Article{barisic2019,
   Author="Barisic, D.  and Stadler, M. B.  and Iurlaro, M.  and Schübeler, D. ",
   Title="{{M}ammalian {I}{S}{W}{I} and {S}{W}{I}/{S}{N}{F} selectively mediate binding of distinct transcription factors}",
   Journal="Nature",
   Year="2019",
   Volume="569",
   Number="7754",
   Pages="136--140",
   Month="05"
}

@Article{iurlaro2021,
   Author="Iurlaro, M.  and Stadler, M. B.  and Masoni, F.  and Jagani, Z.  and Galli, G. G.  and Schübeler, D. ",
   Title="{{M}ammalian {S}{W}{I}/{S}{N}{F} continuously restores local accessibility to chromatin}",
   Journal="Nat Genet",
   Year="2021",
   Volume="53",
   Number="3",
   Pages="279--287",
   Month="03"
}

@Book{agresti2007,
   Author="Agresti, A.",
   Title="An introduction to categorical data analysis",
   Publisher="Wiley-Blackwell",
   Year="2007"
}

@Article{RSAT, 
   Author="Castro-Mondragon, J. A.  and Jaeger, S.  and Thieffry, D.  and Thomas-Chollier, M.  and van Helden, J. ",
   Title="{{R}{S}{A}{T} matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections}",
   Journal="Nucleic Acids Res",
   Year="2017",
   Volume="45",
   Number="13",
   Pages="e119",
   doi = {10.1093/nar/gkx314}, 
   pmid = {28591841}, 
   pmcid = {PMC5737723}, 
}

@Article{encode2012,
	Author = {{The ENCODE Project Consortium}},
	Title = {An integrated encyclopedia of {DNA} elements in the human genome},
	Journal = {Nature},
	Year = {2012},
	Volume = {489},
	Number = {7414},
	Pages = {57--74},
}

