@article{robinson2010,
   Author="Robinson, M. D.  and McCarthy, D. J.  and Smyth, G. K. ",
   Title="{edge{R}: a {B}ioconductor package for differential expression analysis of digital gene expression data}",
   Journal="Bioinformatics",
   Year="2010",
   Volume="26",
   Number="1",
   Pages="139--140",
   Month="Jan"
}

@Article{li2009,
   Author="Li, H.  and Handsaker, B.  and Wysoker, A.  and Fennell, T.  and Ruan, J.  and Homer, N.  and Marth, G.  and Abecasis, G.  and Durbin, R. ",
   Title="{{T}he {S}equence {A}lignment/{M}ap format and {S}{A}{M}tools}",
   Journal="Bioinformatics",
   Year="2009",
   Volume="25",
   Number="16",
   Pages="2078--2079",
   Month="Aug"
}

@Article{oshlack2010,
   Author="Robinson, M. D.  and Oshlack, A. ",
   Title="{{A} scaling normalization method for differential expression analysis of {R}{N}{A}-seq data}",
   Journal="Genome Biol.",
   Year="2010",
   Volume="11",
   Number="3",
   Pages="R25"
}

@Article{robinson2008,
   Author="Robinson, M. D.  and Smyth, G. K. ",
   Title="{{S}mall-sample estimation of negative binomial dispersion, with applications to {S}{A}{G}{E} data}",
   Journal="Biostatistics",
   Year="2008",
   Volume="9",
   Number="2",
   Pages="321--332",
   Month="Apr"
}

@article{benjamini1995,
  title={Controlling the false discovery rate: a practical and powerful approach to multiple testing},
  author={Benjamini, Y. and Hochberg, Y.},
  journal={J. R. Stat. Soc. Series B},
  volume="57",
  pages={289--300},
  year={1995},
  publisher={JSTOR}
}

@article{benjamini2001,
  title={The control of the false discovery rate in multiple testing under dependency},
  author={Benjamini, Y. and Yekutieli, D.},
  journal={Annals of statistics},
  pages={1165--1188},
  year={2001},
  publisher={JSTOR}
}

@Article{liao2013,
   Author="Liao, Y.  and Smyth, G. K.  and Shi, W. ",
   Title="{{T}he {S}ubread aligner: fast, accurate and scalable read mapping by seed-and-vote}",
   Journal="Nucleic Acids Res.",
   Year="2013",
   Volume="41",
   Number="10",
   Pages="e108",
   Month="May"
}


@article{kharchenko2008,
    Author="Kharchenko, P. V.  and Tolstorukov, M. Y.  and Park, P. J. ",
    Title="{{D}esign and analysis of {C}h{I}{P}-seq experiments for {D}{N}{A}-binding proteins}",
    Journal="Nat. Biotechnol.",
    Year="2008",
    Volume="26",
    Number="12",
    Pages="1351--1359",
    Month="Dec"
}

@Article{bourgon2010,
    Author="Bourgon, R.  and Gentleman, R.  and Huber, W. ",
    Title="{{I}ndependent filtering increases detection power for high-throughput experiments}",
    Journal="Proc. Natl. Acad. Sci. U.S.A.",
    Year="2010",
    Volume="107",
    Number="21",
    Pages="9546--9551",
    Month="May"
}

@Article{zhang2008,
   Author="Zhang, Y.  and Liu, T.  and Meyer, C. A.  and Eeckhoute, J.  and Johnson, D. S.  and Bernstein, B. E.  and Nusbaum, C.  and Myers, R. M.  and Brown, M.  and Li, W.  and Liu, X. S. ",
   Title="{{M}odel-based analysis of {C}h{I}{P}-{S}eq ({M}{A}{C}{S})}",
   Journal="Genome Biol.",
   Year="2008",
   Volume="9",
   Number="9",
   Pages="R137"
}

@article{sarkar1997,
    title={The {S}imes method for multiple hypothesis testing with positively dependent test statistics},
    author={Sarkar, S. K. and Chang, C. K.},
    journal={J. Am. Stat. Assoc.},
    pages={1601--1608},
    volume={92},
    number={440},
    year={1997},
    publisher={JSTOR}
}

@article{samuel1996,
    title={Is the {S}imes improved {B}onferroni procedure conservative?},
    author={Samuel-Cahn, E.},
    journal={Biometrika},
    volume={83},
    number={4},
    pages={928--933},
    year={1996},
    publisher={Biometrika Trust}
}

@Article{kim2008,
   Author="Kim, K. I.  and van de Wiel, M. A. ",
   Title="{{E}ffects of dependence in high-dimensional multiple testing problems}",
   Journal="BMC Bioinformatics",
   Year="2008",
   Volume="9",
   Pages="114"
}

@Article{domingo2012,
   Author="Revilla-I-Domingo, R.  and Bilic, I.  and Vilagos, B.  and Tagoh, H.  and Ebert, A.  and Tamir, I. M.  and Smeenk, L.  and Trupke, J.  and Sommer, A.  and Jaritz, M.  and Busslinger, M. ",
   Title="{{T}he {B}-cell identity factor {P}ax5 regulates distinct transcriptional programmes in early and late {B} lymphopoiesis}",
   Journal="EMBO J.",
   Year="2012",
   Volume="31",
   Number="14",
   Pages="3130--3146"
}

@Article{barrett2009,
	Author="Barrett, T.  and Troup, D. B.  and Wilhite, S. E.  and Ledoux, P.  and Rudnev, D.  and Evangelista, C.  and Kim, I. F.  and Soboleva, A.  and Tomashevsky, M.  and Marshall, K. A.  and Phillippy, K. H.  and Sherman, P. M.  and Muertter, R. N.  and Edgar, R. ",
	Title="{{N}{C}{B}{I} {G}{E}{O}: archive for high-throughput functional genomic data}",
	Journal="Nucleic Acids Res.",
	Year="2009",
	Volume="37",
	Number="Database issue",
	Pages="D885--890",
	Month="Jan"
}

@Article{reiner2003,
	Author="Reiner, A.  and Yekutieli, D.  and Benjamini, Y. ",
	Title="{{I}dentifying differentially expressed genes using false discovery rate controlling procedures}",
	Journal="Bioinformatics",
	Year="2003",
	Volume="19",
	Number="3",
	Pages="368--375",
	Month="Feb"
}

@article{simes1986,
	author = {Simes, R. J.}, 
	title = {An improved {B}onferroni procedure for multiple tests of significance}, 
	volume = {73}, 
	number = {3}, 
	pages = {751-754}, 
	year = {1986}, 
	journal = {Biometrika} 
}

@Article{risso2011,
	Author="Risso, D.  and Schwartz, K.  and Sherlock, G.  and Dudoit, S. ",
	Title="{{G}{C}-content normalization for {R}{N}{A}-{S}eq data}",
	Journal="BMC Bioinformatics",
	Year="2011",
	Volume="12",
	Pages="480"
}

@Article{kasper2014genomewide,
    Author="Kasper, L. H.  and Qu, C.  and Obenauer, J. C.  and McGoldrick, D. J.  and Brindle, P. K. ",
    Title="{{G}enome-wide and single-cell analyses reveal a context dependent relationship between {C}{B}{P} recruitment and gene expression}",
    Journal="Nucleic Acids Res.",
    Year="2014",
    Volume="42",
    Number="18",
    Pages="11363--11382",
    Month="Oct"
}


@Article{cheung2011,
	Author="Cheung, M. S.  and Down, T. A.  and Latorre, I.  and Ahringer, J. ",
	Title="{{S}ystematic bias in high-throughput sequencing data and its correction by {B}{E}{A}{D}{S}}",
	Journal="Nucleic Acids Res.",
	Year="2011",
	Volume="39",
	Number="15",
	Pages="e103",
	Month="Aug"
}

@Article{wu2010,
   Author="Wu, S.  and Wang, J.  and Zhao, W.  and Pounds, S.  and Cheng, C. ",
   Title="{{C}h{I}{P}-{P}a{M}: an algorithm to identify protein-{D}{N}{A} interaction using {C}h{I}{P}-{S}eq data}",
   Journal="Theor Biol Med Model",
   Year="2010",
   Volume="7",
   Pages="18"
}

@Article{landt2012,
   Author="Landt, S. G.  and Marinov, G. K.  and Kundaje, A.  and Kheradpour, P.  and Pauli, F.  and Batzoglou, S.  and Bernstein, B. E.  and Bickel, P.  and Brown, J. B.  and Cayting, P.  and Chen, Y.  and Desalvo, G.  and Epstein, C.  and Fisher-Aylor, K. I.  and Euskirchen, G.  and Gerstein, M.  and Gertz, J.  and Hartemink, A. J.  and Hoffman, M. M.  and Iyer, V. R.  and Jung, Y. L.  and Karmakar, S.  and Kellis, M.  and Kharchenko, P. V.  and Li, Q.  and Liu, T.  and Liu, X. S.  and Ma, L.  and Milosavljevic, A.  and Myers, R. M.  and Park, P. J.  and Pazin, M. J.  and Perry, M. D.  and Raha, D.  and Reddy, T. E.  and Rozowsky, J.  and Shoresh, N.  and Sidow, A.  and Slattery, M.  and Stamatoyannopoulos, J. A.  and Tolstorukov, M. Y.  and White, K. P.  and Xi, S.  and Farnham, P. J.  and Lieb, J. D.  and Wold, B. J.  and Snyder, M. ",
   Title="{{C}h{I}{P}-seq guidelines and practices of the {E}{N}{C}{O}{D}{E} and mod{E}{N}{C}{O}{D}{E} consortia}",
   Journal="Genome Res.",
   Year="2012",
   Volume="22",
   Number="9",
   Pages="1813--1831",
   Month="Sep"
}

@Article{mccarthy2012,
   Author="McCarthy, D. J.  and Chen, Y.  and Smyth, G. K. ",
   Title="{{D}ifferential expression analysis of multifactor {R}{N}{A}-{S}eq experiments with respect to biological variation}",
   Journal="Nucleic Acids Res.",
   Year="2012",
   Volume="40",
   Number="10",
   Pages="4288--4297",
   Month="May"
}

@Article{tiwari2012,
   Author="Tiwari, V. K.  and Stadler, M. B.  and Wirbelauer, C.  and Paro, R.  and Schubeler, D.  and Beisel, C. ",
   Title="{{A} chromatin-modifying function of {J}{N}{K} during stem cell differentiation}",
   Journal="Nat. Genet.",
   Year="2012",
   Volume="44",
   Number="1",
   Pages="94--100",
   Month="Jan"
}


@Article{fan1994,
   Author="Fan, J. and Marron, J. S.",
   title="Fast Implementations of Nonparametric Curve Estimators",
   journal="Journal of Computational and Graphical Statistics",
   year=1994,
   volume=3,
   pages="35--56"
}

@Article{lund2012,
   Author="Lund, S. P.  and Nettleton, D.  and McCarthy, D. J.  and Smyth, G. K. ",
   Title="{{D}etecting differential expression in {R}{N}{A}-sequence data using quasi-likelihood with shrunken dispersion estimates}",
   Journal="Stat. Appl. Genet. Mol. Biol.",
   Year="2012",
   Volume="11",
   Number="5",
   Pages=" "
}

@Article{humburg2011,
	Author="Humburg, P.  and Helliwell, C. A.  and Bulger, D.  and Stone, G. ",
	Title="{{C}h{I}{P}seq{R}: analysis of {C}h{I}{P}-seq experiments}",
	Journal="BMC Bioinformatics",
	Year="2011",
	Volume="12",
	Pages="39"
}

@Article{phipson2016,
	Author="Phipson, B. and Lee, S. and Majewski, I. J. and Alexander, W. S. and Smyth, G. K.",
	year = 2016,
	title = "Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression",
    Journal="Ann. Appl. Stat.",
    Volume=10,
    Number=2,
    Pages="946-963"
}

@Article{smyth2004,
	Author="Smyth, G. K. ",
	Title="{{L}inear models and empirical bayes methods for assessing differential expression in microarray experiments}",
	Journal="Stat. Appl. Genet. Mol. Biol.",
	Year="2004",
	Volume="3",
	Pages="Article 3"
}

@Article{ballman2004,
	Author="Ballman, K. V.  and Grill, D. E.  and Oberg, A. L.  and Therneau, T. M. ",
	Title="{{F}aster cyclic loess: normalizing {R}{N}{A} arrays via linear models}",
	Journal="Bioinformatics",
	Year="2004",
	Volume="20",
	Number="16",
	Pages="2778--2786",
	Month="Nov"
}

@Article{law2014,
	Author="Law, C. W.  and Chen, Y.  and Shi, W.  and Smyth, G. K. ",
	Title="{{V}oom: precision weights unlock linear model analysis tools for {R}{N}{A}-seq read counts}",
	Journal="Genome Biol.",
	Year="2014",
	Volume="15",
	Number="2",
	Pages="R29",
	Month="Feb"
}

@Article{lun2014,
	Author="Lun, A. T.  and Smyth, G. K. ",
	Title="{{D}e novo detection of differentially bound regions for {C}h{I}{P}-seq data using peaks and windows: controlling error rates correctly}",
	Journal="Nucleic Acids Res.",
	Year="2014",
	Volume="42",
	Number="11",
	Pages="e95",
	Month="Jul"
}

@Article{lun2016csaw,
    Author="Lun, A. T.  and Smyth, G. K. ",
    Title="{csaw: a {B}ioconductor package for differential binding analysis of {C}h{I}{P}-seq data using sliding windows}",
    Journal="Nucleic Acids Res.",
    Year="2016",
    Volume="44",
    Number="5",
    Pages="e45",
    Month="Mar"
}

@Article{lun2015from,
    author= "Lun, A. T. L. and Smyth, G. K.",
    title="{F}rom reads to regions: a {B}ioconductor workflow to detect differential binding in {C}h{I}{P}-seq data",
    journal="F1000Research",
    volume="4",
    year="2015"
}

@Article{zhang2012,
	Author="Zhang, J. A.  and Mortazavi, A.  and Williams, B. A.  and Wold, B. J.  and Rothenberg, E. V. ",
	Title="{{D}ynamic transformations of genome-wide epigenetic marking and transcriptional control establish {T} cell identity}",
	Journal="Cell",
	Year="2012",
	Volume="149",
	Number="2",
	Pages="467--482",
	Month="Apr"
}

@Article{pal2013,
   Author="Pal, B.  and Bouras, T.  and Shi, W.  and Vaillant, F.  and Sheridan, J. M.  and Fu, N.  and Breslin, K.  and Jiang, K.  and Ritchie, M. E.  and Young, M.  and Lindeman, G. J.  and Smyth, G. K.  and Visvader, J. E. ",
   Title="{{G}lobal changes in the mammary epigenome are induced by hormonal cues and coordinated by {E}zh2}",
   Journal="Cell Rep.",
   Year="2013",
   Volume="3",
   Number="2",
   Pages="411--426",
   Month="Feb"
}

@incollection{chen2014,
	author = {Chen, Y. and Lun, A. T. L. and Smyth, G. K.},
	year = 2014,
	title = {Differential expression analysis of complex {R}{N}{A}-seq experiments using edge{R}},
	booktitle = {Statistical Analysis of Next Generation Sequence Data},
	editor = {Datta, S. and Nettleton, D. S.},
	publisher = {Springer},
	address = {New York}
}

@article {benjamini1997,
	author = {Benjamini, Y. and Hochberg, Y.},
	title = {Multiple hypotheses testing with weights},
	journal = {Scand. J. Stat.},
	volume = {24},
	pages = {407--418},
	year = {1997},
}

@Article{dunham2012,
	Author="ENCODE Project Consortium",
	Title="{{A}n integrated encyclopedia of {D}{N}{A} elements in the human genome}",
	Journal="Nature",
	Year="2012",
	Volume="489",
	Number="7414",
	Pages="57--74",
	Month="Sep"
}

@Article{bonhoure2014quantifying,
    Author="Bonhoure, N.  and Bounova, G.  and Bernasconi, D.  and Praz, V.  and Lammers, F.  and Canella, D.  and Willis, I. M.  and Herr, W.  and Hernandez, N.  and Delorenzi, M.  and Hernandez, N.  and Delorenzi, M.  and Deplancke, B.  and Desvergne, B.  and Guex, N.  and Herr, W.  and Naef, F.  and Rougemont, J.  and Schibler, U.  and Andersin, T.  and Cousin, P.  and Gilardi, F.  and Gos, P.  and Lammers, F.  and Raghav, S.  and Villeneuve, D.  and Fabbretti, R.  and Vlegel, V.  and Xenarios, I.  and Migliavacca, E.  and Praz, V.  and David, F.  and Jarosz, Y.  and Kuznetsov, D.  and Liechti, R.  and Martin, O.  and Delafontaine, J.  and Cajan, J.  and Gustafson, K.  and Krier, I.  and Leleu, M.  and Molina, N.  and Naldi, A.  and Rib, L.  and Symul, L.  and Bounova, G. ",
    Title="{{Q}uantifying {C}h{I}{P}-seq data: a spiking method providing an internal reference for sample-to-sample normalization}",
    Journal="Genome Res.",
    Year="2014",
    Volume="24",
    Number="7",
    Pages="1157--1168",
    Month="Jul"
}

@Article{orlando2014quantitative,
    Author="Orlando, D. A.  and Chen, M. W.  and Brown, V. E.  and Solanki, S.  and Choi, Y. J.  and Olson, E. R.  and Fritz, C. C.  and Bradner, J. E.  and Guenther, M. G. ",
    Title="{{Q}uantitative {C}h{I}{P}-{S}eq normalization reveals global modulation of the epigenome}",
    Journal="Cell Rep.",
    Year="2014",
    Volume="9",
    Number="3",
    Pages="1163--1170",
    Month="Nov"
}

@article{berger1996bioequivalence,
    author = "Berger, R. L. and Hsu, J. C.",
    journal = "Statist. Sci.",
    month = "11",
    number = "4",
    pages = "283--319",
    title = "Bioequivalence trials, intersection-union tests and equivalence confidence sets",
    volume = "11",
    year = "1996"
}

@Article{rossinnes2012differential,
    Author="Ross-Innes, C. S.  and Stark, R.  and Teschendorff, A. E.  and Holmes, K. A.  and Ali, H. R.  and Dunning, M. J.  and Brown, G. D.  and Gojis, O.  and Ellis, I. O.  and Green, A. R.  and Ali, S.  and Chin, S. F.  and Palmieri, C.  and Caldas, C.  and Carroll, J. S. ",
    Title="{{D}ifferential oestrogen receptor binding is associated with clinical outcome in breast cancer}",
    Journal="Nature",
    Year="2012",
    Volume="481",
    Number="7381",
    Pages="389--393",
    Month="Jan"
}

@InCollection{hahne2016visualizing,
    author = {Hahne F. and Ivanek R.},
    editor = {Ewy Math{\'e} and Sean Davis},
    title = {Visualizing Genomic Data Using Gviz and Bioconductor},
    booktitle = {Statistical Genomics: Methods and Protocols},
    year = {2016},
    publisher = {Springer New York},
    address = {New York, NY},
    pages = {335--351},
    isbn = {978-1-4939-3578-9},
    doi = {10.1007/978-1-4939-3578-9_16}
}

@Article{zhu2010chippeakanno,
    Author="Zhu, L. J.  and Gazin, C.  and Lawson, N. D.  and Pages, H.  and Lin, S. M.  and Lapointe, D. S.  and Green, M. R. ",
    Title="{{C}h{I}{P}peak{A}nno: a {B}ioconductor package to annotate {C}h{I}{P}-seq and {C}h{I}{P}-chip data}",
    Journal="BMC Bioinformatics",
    Year="2010",
    Volume="11",
    Pages="237"
}

@Article{hoffman2002changes,
    Author="Hoffmann, R.  and Seidl, T.  and Neeb, M.  and Rolink, A.  and Melchers, F. ",
    Title="{{C}hanges in gene expression profiles in developing {B} cells of murine bone marrow}",
    Journal="Genome Res.",
    Year="2002",
    Volume="12",
    Number="1",
    Pages="98--111",
    Month="Jan"
}

@Article{podojil2003selective,
    Author="Podojil, J. R.  and Sanders, V. M. ",
    Title="{{S}elective regulation of mature {I}g{G}1 transcription by {C}{D}86 and beta 2-adrenergic receptor stimulation}",
    Journal="J. Immunol.",
    Year="2003",
    Volume="170",
    Number="10",
    Pages="5143--5151",
    Month="May"
}


@Article{galvis2015repression,
   Author="Galvis, L. A.  and Holik, A. Z.  and Short, K. M.  and Pasquet, J.  and Lun, A. T.  and Blewitt, M. E.  and Smyth, I. M.  and Ritchie, M. E.  and Asselin-Labat, M. L. ",
   Title="{{R}epression of {I}gf1 expression by {E}zh2 prevents basal cell differentiation in the developing lung}",
   Journal="Development",
   Year="2015",
   Volume="142",
   Number="8",
   Pages="1458--1469",
   Month="Apr"
}

@Article{holik2015transcriptome,
   Author="Holik, A. Z.  and Galvis, L. A.  and Lun, A. T.  and Ritchie, M. E.  and Asselin-Labat, M. L. ",
   Title="{{T}ranscriptome and {H}3{K}27 tri-methylation profiling of {E}zh2-deficient lung epithelium}",
   Journal="Genom Data",
   Year="2015",
   Volume="5",
   Pages="346--351",
   Month="Sep"
}

@Article{liang2012detecting,
   Author="Liang, K.  and Keles, S. ",
   Title="{{D}etecting differential binding of transcription factors with {C}h{I}{P}-seq}",
   Journal="Bioinformatics",
   Year="2012",
   Volume="28",
   Number="1",
   Pages="121--122",
   Month="Jan"
}

