@Comment Review / overview
                  
@Article{pmid19844228,
   Author="Pepke, S.  and Wold, B.  and Mortazavi, A. ",
   Title="{{C}omputation for {C}h{I}{P}-seq and {R}{N}{A}-seq studies}",
   Journal="Nat. Methods",
   Year=2009,
   Volume=6,
   Pages="22--32",
   Month="Nov"
}

                  

@Article{pmid19173299,
   Author="Barski, A.  and Zhao, K. ",
   Title="{{G}enomic location analysis by {C}h{I}{P}-{S}eq}",
   Journal="J. Cell. Biochem.",
   Year=2009,
   Volume=107,
   Pages="11--18",
   Month="May"
}

@Article{pmid19275939,
   Author="Schmidt, D.  and Wilson, M. D.  and Spyrou, C.  and Brown,
                  G. D.  and Hadfield, J.  and Odom, D. T. ",
   Title="{{C}h{I}{P}-seq: using high-throughput sequencing to
                  discover protein-{D}{N}{A} interactions}",
   Journal="Methods",
   Year="2009",
   Volume="48",
   Pages="240--248",
   Month="Jul"
}

                  
@Comment Bioinformatics

@article{Park,
  author = {P. V. Kharchenko and M. Y. Tolstorukov and P. J. Park},
  title = {Design and Analysis of Ch{IP} experiments for {DNA}--binding proteins},
  journal = {Nature Biotechnology},
  year = 2008,
  pages = {1351--1359},
  volume = 26
}

@Comment statistical methods

@article{Waterman,
  title={Genomic mapping by fingerprinting random clones: a mathematical analysis},
  author={Lander, E. S. and Waterman, M. S.},
  journal={Genomics},
  volume=2,
  number=3,
  pages={231--239},
  year=1988
}

@article{GentGeyer,
  author = {R. Gentleman and C. Geyer},
  journal = {Biometrika},
  title = {Maximum likelihood for interval censored data: consistency and computation}, 
   year = 1994,
   volume = 81,
   pages = {618--623}
}

@Comment Examples

% 19212405 
@Article{pmid19212405,
   Author="Visel, A.  and Blow, M. J.  and Li, Z.  and Zhang, T.  and Akiyama, J. A.  and Holt, A.  and Plajzer-Frick, I.  and Shoukry, M.  and Wright, C.  and Chen, F.  and Afzal, V.  and Ren, B.  and Rubin, E. M.  and Pennacchio, L. A. ",
   Title="{{C}h{I}{P}-seq accurately predicts tissue-specific activity of enhancers}",
   Journal="Nature",
   Year=2009,
   Volume=457,
   Pages="854--858",
   Month="Feb"
}

@Article{pmid20412780,
   Author="Cao, Y.  and Yao, Z.  and Sarkar, D.  and Lawrence, M.  and Sanchez, G. J.  and Parker, M. H.  and MacQuarrie, K. L.  and Davison, J.  and Morgan, M. T.  and Ruzzo, W. L.  and Gentleman, R. C.  and Tapscott, S. J. ",
   Title="{{G}enome-wide {M}yo{D} binding in skeletal muscle cells: a potential for broad cellular reprogramming}",
   Journal="Dev. Cell",
   Year=2010,
   Volume=18,
   Pages="662--674",
   Month="Apr"
}
                  

@Article{pmid18555785,
   Author="Chen, X.  and Xu, H.  and Yuan, P.  and Fang, F.  and Huss, M.  and Vega, V. B.  and Wong, E.  and Orlov, Y. L.  and Zhang, W.  and Jiang, J.  and Loh, Y. H.  and Yeo, H. C.  and Yeo, Z. X.  and Narang, V.  and Govindarajan, K. R.  and Leong, B.  and Shahab, A.  and Ruan, Y.  and Bourque, G.  and Sung, W. K.  and Clarke, N. D.  and Wei, C. L.  and Ng, H. H. ",
   Title="{{I}ntegration of external signaling pathways with the core transcriptional network in embryonic stem cells}",
   Journal="Cell",
   Year=2008,
   Volume=133,
   Pages="1106--1117",
   Month="Jun"
}
                  
@Article{pmid19122651,
   Author="Rozowsky, J.  and Euskirchen, G.  and Auerbach, R. K.  and Zhang, Z. D.  and Gibson, T.  and Bjornson, R.  and Carriero, N.  and Snyder, M.  and Gerstein, M. B. ",
   Title="{{P}eak{S}eq enables systematic scoring of {C}h{I}{P}-seq experiments relative to controls}",
   Journal="Nat. Biotechnol.",
   Year=2009,
   Volume=27,
   Pages="66--75",
   Month="Jan"
}

@article{Valouev2008,
  author = {A. Valouev and D. S. Johnson and A. Sundquist and C. Medina and E. Anton and S. Batzoglou and R. M. Myers and A. Sidow},
  title = {Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.},
  journal = {Nat Methods},
  year = 2008,
  volume = 5,
  number = 9,
  pages = {829--834},
  url = {http://dx.doi.org/10.1038/nmeth.1246},
  doi = {http://dx.doi.org/10.1038/nmeth.1246}
}
                  
@article{NARchipseq,
  author = {R. Jothi and S. Cuddapah and A. Barski and K. Cui and K. Zhao},
  journal = {NAR},
  year = 2008,
  volume = 36,
  pages = {5221--31},
  title = {Genome-wide identification of in vivo protein-{DNA} binding sites 
    from {ChIP-Seq} data},
}

@article{Johnson2007,
  author = {D. S. Johnson and A. Mortazavi and R. M. Myers and B. Wold},
  title = {Genome-wide mapping of in vivo protein-DNA interactions.},
  journal = {Science},
  year = 2007,
  volume = 316,
  number = 5830,
  pages = {1497--1502},
  url = {http://www.sciencemag.org/cgi/content/abstract/316/5830/1497},
}
                  
@Article{pmid17558387,
   Author="Robertson, G.  and Hirst, M.  and Bainbridge, M.  and Bilenky, M.  and Zhao, Y.  and Zeng, T.  and Euskirchen, G.  and Bernier, B.  and Varhol, R.  and Delaney, A.  and Thiessen, N.  and Griffith, O. L.  and He, A.  and Marra, M.  and Snyder, M.  and Jones, S. ",
   Title="{{G}enome-wide profiles of {S}{T}{A}{T}1 {D}{N}{A} association using chromatin immunoprecipitation and massively parallel sequencing}",
   Journal="Nat. Methods",
   Year=2007,
   Volume=4,
   Pages="651--657",
   Month="Aug"
}

@Article{pmid19736561,
   Author="Park, P. J. ",
   Title="{{C}h{I}{P}-seq: advantages and challenges of a maturing technology}",
   Journal="Nat. Rev. Genet.",
   Year=2009,
   Volume=10,
   Pages="669--680",
   Month="Oct"
}

@Article{pmid18798982,
   Author="Zhang, Y.  and Liu, T.  and Meyer, C. A.  and Eeckhoute, J.  and Johnson, D. S.  and Bernstein, B. E.  and Nussbaum, 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,
   Pages="R137"
}

@article{ElodiePortales-Casamar01012010,
author = {Portales-Casamar, E. and others},
title = {{JASPAR 2010: the greatly expanded open-access database of
                  transcription factor binding profiles}},
journal = {Nucl. Acids Res.},
volume = 38,
number = {suppl 1},
pages = {D105-110},
year = 2010,
eprint = {http://nar.oxfordjournals.org/cgi/reprint/38/suppl_1/D105.pdf}
}

@article{Schones2008887,
title = "Dynamic Regulation of Nucleosome Positioning in the Human Genome",
journal = "Cell",
volume = 132,
number = 5,
pages = "887 - 898",
year = 2008,
issn = "0092-8674",
author = "D. E. Schones and K. Cui and S. Cuddapah and T.-Y. Roh and A. Barski and Z. Wang and G. Wei and K. Zhao",
keywords = "DNA",
keywords = "SIGNALING"
}



@Article{pmid18987734,
   Author="Bentley, D. R.  et al",
   Title="{{A}ccurate whole human genome sequencing using reversible terminator chemistry}",
   Journal="Nature",
   Year=2008,
   Volume=456,
   Pages="53--59",
   Month="Nov"
}

