
@Book{biocbook2005,
  editor =	 {Robert Gentleman and Vincent Carey and Wolfgang
                  Huber and Rafael Irizarry and Sandrine Dudoit},
  title =	 {Bioinformatics and Computational Biology Solutions
                  Using R and Bioconductor},
  publisher =	 {Springer},
  year =	 {2005}
}

@Article{bioconductor,
  author =	 {Robert C. Gentleman and Vincent J. Carey and Douglas
                  J. Bates and Benjamin M. Bolstad and Marcel Dettling
                  and Sandrine Dudoit and Byron Ellis and Laurent
                  Gautier and Yongchao Ge and Jeff Gentry and Kurt
                  Hornik and Torsten Hothorn and Wolfgang Huber and
                  Stefano Iacus and Rafael Irizarry and Friedrich
                  Leisch and Cheng Li and Martin Maechler and Anthony
                  J. Rossini and Guenther Sawitzki and Colin Smith and
                  Gordon K. Smyth and Luke Tierney and Yee Hwa Yang
                  and Jianhua Zhang},
  title =	 {Bioconductor: Open software development for
                  computational biology and bioinformatics},
  journal =	 {Genome Biology},
  volume =	 {5},
  year =	 {2004},
  pages =	 {R80}
}

@Manual{Biostrings,
  title = {Biostrings: String objects representing biological sequences, and matching algorithms},
  author = {H. Pages and R. Gentleman and P. Aboyoun and S. DebRoy},
  year = {2008},
  note = {R package version 2.9.29},
}

@INPROCEEDINGS{limma05,
  editor = {Robert Gentleman and Vincent Carey and Wolfgang Huber 
             and Rafael Irizarry and Sandrine Dudoit},
  booktitle = {Bioinformatics and Computational Biology Solutions
               Using R and Bioconductor},
  publisher = {Springer},
  year = {2005},
  author = {Gordon K. Smyth},
  title = {Limma: linear models for microarray data},
  pages = {397--420},
}

@phdthesis{BourgonPhD,
  author = {Richard W. Bourgon},
  title = {Chromatin-immunoprecipitation and high-density tiling microarrays: a generative model, methods for analysis, and methodology assessment in the absence of a ''gold standard''},
  school = {University of California, Berkley},
  address = {Berkley, California, USA},
  year = {2006},
  url = {http://www.ebi.ac.uk/~bourgon/papers/bourgon_dissertation_public.pdf},
}

@article{HuberVSN,
  title =	 {Variance Stabilization Applied to Microarray Data
                  Calibration and to the Quantification of
                  Differential Expression},
  author =	 {Wolfgang Huber and Anja von Heydebreck and Holger
                  {S\"ultmann} and Annemarie Poustka and Martin
                  Vingron},
  journal =	 {Bioinformatics},
  year =	 {2002},
  volume =	 {18},
  pages =	 {S96--S104},
}

@Article{Parkinson2009,
  author =       {Helen Parkinson and Misha Kapushesky and Nikolay Kolesnikov and Gabriella Rustici and Mohammad Shojatalab and Niran Abeygunawardena and Hugo Berube and Miroslaw Dylag and Ibrahim Emam and Anna Farne and Ele Holloway and Margus Lukk and James Malone and Roby Mani and Ekaterina Pilicheva and Tim F Rayner and Faisal Rezwan and Anjan Sharma and Eleanor Williams and Xiangqun Zheng Bradley and Tomasz Adamusiak and Marco Brandizi and Tony Burdett and Richard Coulson and Maria Krestyaninova and Pavel Kurnosov and Eamonn Maguire and Sudeshna Guha Neogi and Philippe Rocca-Serra and Susanna-Assunta Sansone and Nataliya Sklyar and Mengyao Zhao and Ugis Sarkans and Alvis Brazma},
  title =        {{ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.}},
  journal =      {Nucleic Acids Research},
  year =         {2009},
  month =        {Jan},
  volume =       {37},
  number =       {Database issue},
  pages =        {D868--D872},
  PMID =         {19015125},
  url =          {http://www.ebi.ac.uk/arrayexpress},
}

@Article{Pozhitkov2007,
  author =       {Alex E Pozhitkov and Diethard Tautz and Peter A Noble},
  title =        {Oligonucleotide microarrays: widely applied--poorly understood.},
  journal =      {Brief Funct Genomic Proteomic},
  year =         {2007},
  month =        {Jun},
  volume =       {6},
  number =       {2},
  pages =        {141--148},
  PMID =         {17644526},
}

@article{Ringo2007,
  title = {Ringo - an {R/Bioconductor} package for analyzing {ChIP-chip} readouts},
  author = {Joern Toedling and Oleg Sklyar and Tammo Krueger and Jenny J Fischer and Silke Sperling and Wolfgang Huber},
  journal = {BMC Bioinformatics},
  year = {2007},
  volume = {8},
  pages = {221},
}

@Article{Schmidt2008,
  author =       {Dominic Schmidt and Rory Stark and Michael D Wilson and Gordon D Brown and Duncan T Odom},
  title =        {{Genome-scale validation of deep-sequencing libraries.}},
  journal =      {PLoS ONE},
  year =         {2008},
  month =        {},
  volume =       {3},
  number =       {11},
  pages =        {e3713},
  PMID =         {19002256},
}

% the Exonerate paper:
@article{Slater2005,
  title = {Automated generation of heuristics for biological sequence comparison},
  author = {Guy St C Slater and Ewan Birney},
  journal = {BMC Bioinformatics},
  year = {2005},
  volume = {6},
  pages = {31},
}

@Article{Squazzo2006,
  author =       {Sharon L Squazzo and Henriette {O'Geen} and Vitalina M Komashko and Sheryl R Krig and Victor X Jin and Sung-wook Jang and Raphael Margueron and Danny Reinberg and Roland Green and Peggy J Farnham},
  title =        {Suz12 binds to silenced regions of the genome in a cell-type-specific manner.},
  journal =      {Genome Res},
  year =         {2006},
  volume =       {16},
  number =       {7},
  pages =        {890--900},
  PMID =         {16751344},
}

@Article{Toedling2008,
    author =    {Joern Toedling and Wolfgang Huber},
    journal =   {PLoS Computational Biology},
    publisher = {Public Library of Science},
    title =     {{Analyzing ChIP-chip Data Using Bioconductor}},
    year =      {2008},
    month =     {Nov},
    volume =    {4},
    pages =     {e1000227},
    number =    {11},
    PMID =      {19043553},
}
