@string{GB =    {Genome Biology}}

@Article{BioC2004,
  author =	 {Robert C Gentleman and Vincent J. Carey and Douglas
                  M. Bates and others},
  title =	 {Bioconductor: Open software development for
                  computational biology and bioinformatics},
  journal =	 {Genome Biology},
  volume =	 5,
  year =	 2004,
  pages =	 {R80},
  url =		 {http://genomebiology.com/2004/5/10/R80},
}

@Article{Boutros2004,
  Author =	 "Boutros, Michael and Kiger, Amy A and Armknecht,
                  Susan and Kerr, Kim and Hild, Marc and Koch, Britta
                  and Haas, Stefan A and Consortium, Heidelberg Fly
                  Array and Paro, Renato and Perrimon, Norbert",
  Title =	 "{Genome-wide RNAi analysis of growth and viability
                  in Drosophila cells}",
  Journal =	 "Science",
  Year =	 2004,
  Volume =	 303,
  Number =	 5659,
  Pages =	 "832--835",
}

@Article{Boutros2006,
  author =	 "Boutros, M and {Br\'as}, LP and Huber, W",
  title =	 "Analysis of cell-based {RNAi} screens",
  journal =	 {Genome Biology},
  year =	 2006,
  volume =	 7,
  pages =	 "R66",
}

@Article{Brideau2003,
  author =	 {Brideau, C and Gunter, B and Pikounis, B and Liaw,
                  A},
  title =	 {Improved statistical methods for hit selection in
                  high-throughput screening},
  journal =	 {J. Biomol. Screen},
  year =	 2003,
  volume =	 8,
  pages =	 {634--647},
}

@Article{Ensembl2006,
  Author =	 "Birney, E and Andrews, D and Caccamo, M and Chen, Y
                  and Clarke, L and Coates, G and Cox, T and
                  Cunningham, F and Curwen, V and Cutts, T and Down, T
                  and Durbin, R and Fernandez-Suarez, X M and Flicek,
                  P and Graf, S and Hammond, M and Herrero, J and
                  Howe, K and Iyer, V and Jekosch, K and Kahari, A and
                  Kasprzyk, A and Keefe, D and Kokocinski, F and
                  Kulesha, E and London, D and Longden, I and Melsopp,
                  C and Meidl, P and Overduin, B and Parker, A and
                  Proctor, G and Prlic, A and Rae, M and Rios, D and
                  Redmond, S and Schuster, M and Sealy, I and Searle,
                  S and Severin, J and Slater, G and Smedley, D and
                  Smith, J and Stabenau, A and Stalker, J and
                  Trevanion, S and Ureta-Vidal, A and Vogel, J and
                  White, S and Woodwark, C and Hubbard, T J P",
  Title =	 "{Ensembl 2006}",
  Journal =	 "Nucleic Acids Res",
  Year =	 2006,
  Volume =	 34,
  Number =	 "Database issue",
  Pages =	 "556--561",
}

@Article{GO,
  Author =	 "Harris, M A and Clark, J and Ireland, A and Lomax, J
                  and Ashburner, M and Foulger, R and Eilbeck, K and
                  Lewis, S and Marshall, B and Mungall, C and Richter,
                  J and Rubin, G M and Blake, J A and Bult, C and
                  Dolan, M and Drabkin, H and Eppig, J T and Hill, D P
                  and Ni, L and Ringwald, M and Balakrishnan, R and
                  Cherry, J M and Christie, K R and Costanzo, M C and
                  Dwight, S S and Engel, S and Fisk, D G and
                  Hirschman, J E and Hong, E L and Nash, R S and
                  Sethuraman, A and Theesfeld, C L and Botstein, D and
                  Dolinski, K and Feierbach, B and Berardini, T and
                  Mundodi, S and Rhee, S Y and Apweiler, R and
                  Barrell, D and Camon, E and Dimmer, E and Lee, V and
                  Chisholm, R and Gaudet, P and Kibbe, W and Kishore,
                  R and Schwarz, E M and Sternberg, P and Gwinn, M and
                  Hannick, L and Wortman, J and Berriman, M and Wood,
                  V and de la Cruz, N and Tonellato, P and Jaiswal, P
                  and Seigfried, T and White, R",
  Title =	 "{The Gene Ontology (GO) database and informatics
                  resource}",
  Journal =	 "Nucleic Acids Res",
  Year =	 2004,
  Volume =	 32,
  Number =	 "Database issue",
  Pages =	 "258--261",
}

@Article{Gentleman2004RepRes,
  author =	 {Robert Gentleman},
  title =	 {Reproducible Research: A Bioinformatics Case Study},
  journal =	 {Statistical Applications in Genetics and Molecular
                  Biology},
  year =	 2004,
  volume =	 3
}

@Manual{GentlemanCategories,
  title =	 {Category: Category Analysis},
  author =	 {R. Gentleman},
  year =	 2006,
  note =	 {R package version 1.3.3},
}

@article{Huber2002ismb,
  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 Suppl. 1},
  pages =	 {S96-S104},
}

@Article{Kasprzyk2004,
  Author =	 "Kasprzyk, Arek and Keefe, Damian and Smedley, Damian
                  and London, Darin and Spooner, William and Melsopp,
                  Craig and Hammond, Martin and Rocca-Serra, Philippe
                  and Cox, Tony and Birney, Ewan",
  Title =	 "{EnsMart: a generic system for fast and flexible
                  access to biological data}",
  Journal =	 "Genome Res",
  Year =	 2004,
  Volume =	 14,
  Number =	 1,
  Pages =	 "160--169",
  Month =	 "Jan"
}

@Article{Malo2006,
  Author =	 "Malo, Nathalie and Hanley, James and Cerquozzi,
                  Sonia and Pelletier, Jerry and Nadon, Robert",
  Title =	 "{Statistical practice in high-throughput screening
                  data analysis}",
  Journal =	 "Nature Biotechnology",
  Year =	 2006,
  Volume =	 24,
  Number =	 2,
  Pages =	 "167--175",
}

@Article{Oldenburg1999,
  Author =	 "JH Zhang and TD Chung and KR Oldenburg",
  Title =	 "{A Simple Statistical Parameter for Use in
                  Evaluation and Validation of High Throughput
                  Screening Assays}",
  Journal =	 "J Biomol Screen",
  Year =	 1999,
  Volume =	 4,
  Number =	 2,
  Pages =	 "67--73"
}

@Book{Tukey1977,
  author =	 {J.W. Tukey},
  title =	 {Exploratory Data Analysis},
  publisher =	 {Addison-Wesley},
  year =	 1977,
  address =	 "Cambridge, MA",
}

@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 =	 GB,
  volume =	 5,
  year =	 2004,
  pages =	 {R80},
  url =		 {http://genomebiology.com/2004/5/10/R80}
}

% Tukey's median polish procedure

@Article{biomaRt2005,
  Author =	 "Durinck, Steffen and Moreau, Yves and Kasprzyk, Arek
                  and Davis, Sean and De Moor, Bart and Brazma, Alvis
                  and Huber, Wolfgang",
  Title =	 "{BioMart and Bioconductor: a powerful link between
                  biological databases and microarray data analysis}",
  Journal =	 "Bioinformatics",
  Year =	 2005,
  Volume =	 21,
  Number =	 16,
  Pages =	 "3439--3440",
  Month =	 "Aug"
}
