% 19689216
@Article{pmid19689216,
   Author="Sammeth, M. ",
   Title="{{C}omplete alternative splicing events are bubbles in splicing graphs}",
   Journal="J. Comput. Biol.",
   Year="2009",
   Volume="16",
   Pages="1117--1140",
   Month="Aug"
}


@Article{goseq,
    title = {Gene ontology analysis for RNA-seq: accounting for selection bias},
    author = {Matthew D Young and Matthew J Wakefield and Gordon K Smyth and Alicia Oshlack},
    journal = {Genome Biology},
    volume = {11},
    pages = {R14},
    year = {2010},
  }


% 19029915
@Article{pmid19029915,
   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",
   Pages="1351--1359",
   Month="Dec",
   Note={[PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2597701}{PMC2597701}] [DOI:\href{http://dx.doi.org/10.1038/nbt.1508}{10.1038/nbt.1508}] [PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/19029915}{19029915}] }
}
% 15550541
@Article{pmid15550541,
   Author="Sabo, P. J.  and Hawrylycz, M.  and Wallace, J. C.  and Humbert, R.  and Yu, M.  and Shafer, A.  and Kawamoto, J.  and Hall, R.  and Mack, J.  and Dorschner, M. O.  and McArthur, M.  and Stamatoyannopoulos, J. A. ",
   Title="{{D}iscovery of functional noncoding elements by digital analysis of chromatin structure}",
   Journal="Proc. Natl. Acad. Sci. U.S.A.",
   Year="2004",
   Volume="101",
   Pages="16837--16842",
   Month="Nov"
}
% 21526222
@Article{pmid21526222,
   Author="Myers, R. M.  and Stamatoyannopoulos, J.  and Snyder, M.  and \ldots.  and Good, P. J. ",
   Title="{{A} user's guide to the encyclopedia of {D}{N}{A} elements ({E}{N}{C}{O}{D}{E})}",
   Journal="PLoS Biol.",
   Year="2011",
   Volume="9",
   Pages="e1001046",
   Month="Apr",
   Note={[PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3079585}{PMC3079585}] [DOI:\href{http://dx.doi.org/10.1371/journal.pbio.1001046}{10.1371/journal.pbio.1001046}] [PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/21526222}{21526222}] }
}

% 21179089
@Article{pmid21179089,
   Author="Kharchenko, P. V.  and Alekseyenko, A. A.  and Schwartz, Y. B.  and Minoda, A.  and Riddle, N. C.  and Ernst, J.  and Sabo, P. J.  and Larschan, E.  and Gorchakov, A. A.  and Gu, T.  and Linder-Basso, D.  and Plachetka, A.  and Shanower, G.  and Tolstorukov, M. Y.  and Luquette, L. J.  and Xi, R.  and Jung, Y. L.  and Park, R. W.  and Bishop, E. P.  and Canfield, T. K.  and Sandstrom, R.  and Thurman, R. E.  and MacAlpine, D. M.  and Stamatoyannopoulos, J. A.  and Kellis, M.  and Elgin, S. C.  and Kuroda, M. I.  and Pirrotta, V.  and Karpen, G. H.  and Park, P. J. ",
   Title="{{C}omprehensive analysis of the chromatin landscape in {D}rosophila melanogaster}",
   Journal="Nature",
   Year="2011",
   Volume="471",
   Pages="480--485",
   Month="Mar",
   Note={[PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109908}{PMC3109908}] [DOI:\href{http://dx.doi.org/10.1038/nature09725}{10.1038/nature09725}] [PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/21179089}{21179089}] }
}

% 19844228
@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",
   Note={[DOI:\href{http://dx.doi.org/10.1038/nmeth.1371}{10.1038/nmeth.1371}] [PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/19844228}{19844228}] }
}

% 19736561
@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",
   Note={[PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3191340}{PMC3191340}] [DOI:\href{http://dx.doi.org/10.1038/nrg2641}{10.1038/nrg2641}] [PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/19736561}{19736561}] }
}

% 21356108
@Article{pmid21356108,
   Author="Ho, J. W.  and Bishop, E.  and Karchenko, P. V.  and Negre, N.  and White, K. P.  and Park, P. J. ",
   Title="{{C}h{I}{P}-chip versus {C}h{I}{P}-seq: lessons for experimental design and data analysis}",
   Journal="BMC Genomics",
   Year="2011",
   Volume="12",
   Pages="134",
   Note={[PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3053263}{PMC3053263}] [DOI:\href{http://dx.doi.org/10.1186/1471-2164-12-134}{10.1186/1471-2164-12-134}] [PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/21356108}{21356108}] }
}

@Article{pmid18798982,
   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,
   Pages="R137",
   Note={[PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2592715}{PMC2592715}] [DOI:\href{http://dx.doi.org/10.1186/gb-2008-9-9-r137}{10.1186/gb-2008-9-9-r137}] [PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/18798982}{18798982}] }
}


@Book{Matloff2011,
  Author = 	 {Matloff, N.},
  title = 	 {The Art of {R} Programming},
  publisher = 	 {No Starch Pess},
  year = 	 2011,
  pages  = 373
}

@book{R:Dalgaard:2008,
  author = {Peter Dalgaard},
  title = {Introductory Statistics with {R}},
  edition = {2nd},
  year = 2008,
  publisher = {Springer},
  isbn = {978-0-387-79053-4},
  pages = 380,
  url = {http://www.biostat.ku.dk/~pd/ISwR.html},
  publisherurl = {http://www.springer.com/statistics/computational/book/978-0-387-79053-4},
  orderinfo = {springer.txt},
  abstract = {This book provides an elementary-level introduction to
                  R, targeting both non-statistician scientists in
                  various fields and students of statistics. The main
                  mode of presentation is via code examples with liberal
                  commenting of the code and the output, from the
                  computational as well as the statistical viewpoint. A
                  supplementary R package can be downloaded and contains
                  the data sets.  The statistical methodology includes
                  statistical standard distributions, one- and
                  two-sample tests with continuous data, regression
                  analysis, one- and two-way analysis of variance,
                  regression analysis, analysis of tabular data, and
                  sample size calculations. In addition, the last six
                  chapters contain introductions to multiple linear
                  regression analysis, linear models in general,
                  logistic regression, survival analysis, Poisson
                  regression, and nonlinear regression.}
}

@book{R:Gentleman:2008b,
  author = {Robert Gentleman},
  title = {{R} Programming for Bioinformatics},
  publisher = {Chapman \& Hall/CRC},
  year = 2008,
  series = {Computer Science \& Data Analysis},
  address = {Boca Raton, FL},
  isbn = {978-1-420-06367-7},
  url = {http://www.bioconductor.org/pub/RBioinf/},
  publisherurl = {http://crcpress.com/shopping_cart/products/product_detail.asp?sku=C6367},
  abstract = {Thanks to its data handling and modeling capabilities
                  and its flexibility, R is becoming the most widely
                  used software in bioinformatics.  R Programming for
                  Bioinformatics builds the programming skills needed to
                  use R for solving bioinformatics and computational
                  biology problems.  Drawing on the author's experiences
                  as an R expert, the book begins with coverage on the
                  general properties of the R language, several unique
                  programming aspects of R, and object-oriented
                  programming in R. It presents methods for data input
                  and output as well as database interactions. The
                  author also examines different facets of string
                  handling and manipulations, discusses the interfacing
                  of R with other languages, and describes how to write
                  software packages. He concludes with a discussion on
                  the debugging and profiling of R code.},
  orderinfo = {crcpress.txt}
}

@book{R:Chambers:2008,
  author = {John M. Chambers},
  title = {Software for Data Analysis: Programming with {R}},
  publisher = {Springer},
  year = 2008,
  address = {New York},
  isbn = {978-0-387-75935-7},
  url = {http://stat.stanford.edu/~jmc4/Rbook/},
  publisherurl = {http://www.springer.com/statistics/computational/book/978-0-387-75935-7},
  abstract = {The R version of S4 and other R techniques.  This book
                  guides the reader in programming with R, from
                  interactive use and writing simple functions to the
                  design of R packages and intersystem interfaces.},
  orderinfo = {springer.txt}
}


% 20080505
@Article{pmid20080505,
   Author="Li, H.  and Durbin, R. ",
   Title="{{F}ast and accurate long-read alignment with {B}urrows-{W}heeler transform}",
   Journal="Bioinformatics",
   Year="2010",
   Volume="26",
   Pages="589--595",
   Month="Mar"
}

% 19451168
@Article{pmid19451168,
   Author="Li, H.  and Durbin, R. ",
   Title="{{F}ast and accurate short read alignment with {B}urrows-{W}heeler transform}",
   Journal="Bioinformatics",
   Year="2009",
   Volume="25",
   Pages="1754--1760",
   Month="Jul"
}

@Article{pmid19261174,
   Author="Langmead, B.  and Trapnell, C.  and Pop, M.  and Salzberg, S. L. ",
   Title="{{U}ltrafast and memory-efficient alignment of short {D}{N}{A} sequences to the human genome}",
   Journal="Genome Biol.",
   Year="2009",
   Volume="10",
   Pages="R25"
}

@article{Brooks2010,
  author =	 {Brooks, A. N. and Yang, L. and Duff, M. O. and
                  Hansen, K. D. and Park, J. W. and Dudoit, S. and
                  Brenner, S. E. and Graveley, B. R.},
  doi =		 {10.1101/gr.108662.110},
  issn =	 {1088-9051},
  journal =	 {Genome Research},
  pages =	 {193--202},
  title =	 {{Conservation of an RNA regulatory map between
                  Drosophila and mammals}},
  url =          {http://genome.cshlp.org/cgi/doi/10.1101/gr.108662.110},
  year =	 2011
}

@Article{AndersHuber2010,
    title = {Differential expression analysis for sequence count data},
    author = {Simon Anders and Wolfgang Huber},
    year = 2010,
    journal = {Genome Biology},
    volume = 11,
    pages = {R106},
    doi = {10.1186/gb-2010-11-10-r106},
    url = {http://genomebiology.com/2010/11/10/R106/},
  }

@Article{pmid19910308,
   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",
   Pages="139--140",
   Month="Jan"
}
