

@string{PNAS="Proceedings of the National Academy of Sciences"}

@article{Isakoff2005,
 author = {Michael S. Isakoff, Courtney G. Sansam, Pablo Tamayo, Aravind Subramanian, Julia A. Evans,
           Christine M. Fillmore, Xi Wang, Jaclyn A. Biegel, Scott L. Pomeroy, Jill P. Mesirov,
           and Charles W. M. Roberts},
  title = {Inactivation of the Snf5 tumor suppressor stimulates cell cycle progression and cooperates with
           p53 loss in oncogenic transformation},
 journal = {PNAS},
 volume = {102},
 pages = {17745 - 17750},
 year = {2005}, 
 month = {December},
},

@article{Ghazalpour2005,
 author = {Anatole Ghazalpour, Sudheer Doss, Sonal S Sheth, Leslie A Ingram-Drake, Eric E Schadt,
           Aldons J Lusis and Thomas A Drake},
 title = {Genomic analysis of metabolic pathway gene expression in mice},
 journal = {Genome Biology},
 volume = {6:R59},
 year = {2005},
},

@article{Creighton2006,
 author = {Chad J Creighton, Kevin E Cordero, Jose M Larios, Rebecca S Miller, Michael D Johnson,
           Arul M Chinnaiyan, Marc E Lippman and James M Rae},
 title = {Genes regulated by estrogen in breast tumor cells in vitro are similarly regulated 
          in vivo in tumor xenografts and human breast tumors},
 journal = {Genome Biology},
 volume = {7:R28},
 year = {2006},
},

@article{Majumder2004,
 author = {P. K. Majumder and P. G. Febbo and R. Bikoff and others},
 title = { m{TOR} inhibition reverses Akt-dependent prostate intraepithelial 
  neoplasia through regulation of apoptotic and {HIF-1}-dependent pathways},
 journal = {Nature Medicine},
 volume =  {10}, 
 pages = {594--601},
 year = {2004},
},


@Article{Kim2005,
  author = 	 {Seon-Young Kim and David J Volsky},
  title = 	 {PAGE: Parametric Analysis of Gene Set Enrichment},
  journal = 	 {BMC Bioinformatics},
  year = 	 {2005},
  volume = 	 {6;144},
  month = 	 {June},
},

@Article{Yeoh2002,
  author = 	 {E-J. Yeoh and M. E. Ross and S. A. Shurtleff and others},
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  journal = 	 {Cancer Cell},
  year = 	 {2002},
  volume = 	 {1},
  pages = 	 {133-143},
  month = 	 {March},
},

@Book{Mardia,
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@article{newton:kendziorski:richmond:blattner:tsui:2001,
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  title =	 {On differential variability of expression ratios:
                  Improving statistical inference about gene
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  year =	 {2001},
  journal =	 {Journal of Computational Biology},
  volume =	 {8},
  pages =	 {37-52},
},

@article{KEGG,
  author =	 {Kanehisa, M. and Goto, S.},
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@Article{GO,
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  title = 	 {{G}ene {O}ntology: tool for the unification of biology},
  journal = 	 {Nature Genetics},
  year = 	 {2000},
  volume = 	 {25},
  pages = 	 {25-29},
},

@Book{Johnson,
  author = 	 {Richard A. Johnson and Dean W. Wichern},
  title = 	 {Applied Multivariate},
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  year = 	 {1988},
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@article{Subramanian2005,
author={A. Subramanian and P. Tamayo and V. K. Mootha and others},
title={Gene set enrichment analysis: A knowledge-based approach for 
   interpreting genome-wide expression profiles},
journal=PNAS,
year={2005},
volume={102},
number={43},
pages={15545--15550},
},

@article{Tian2005,
  author={Tian, L. and Greenberg, S. A. and Kong, S. W. and others},
  title={Discovering statistically significant pathways in expression profiling studies},
  journal=PNAS,
  year={2005},
  volume={102},
  number={38},
  pages={13544--13549},
},

@article{Gentleman2005,
  author={Gentleman, R. and Newton, M. and Speed, T. P. and Dudoit, S. and Miller, A.},
  title={Using Categories to Model Genomic Data},
  journal={Manuscript},
  month={February},
  year={2005},
},

@article{Mootha2003,
  author =	 {Mootha, V. K. and Lindgren, C. M. and others},
  title =	 {{PGC}-1$\alpha$-responsive genes involved in
                  oxidative phosphorylation are coordinately
                  downregulated in human diabetes},
  journal =	 {Nature Genetics},
  year =	 {2003},
  volume =	 {34},
  pages =	 {267--273}
},

@Article{Chiaretti2004,
 author = { S. Chiaretti and X Li and R Gentleman and A Vitale and 
M. Vignetti and F. Mandelli and J.  Ritz and and R. Foa},
  year = {2004},
 title = {Gene expression profile of adult {T}-cell acute lymphocytic leukemia
identifies distinct subsets of patients with different response to therapy
and survival},
  journal = {Blood},
  pages = {2771--2778},
  volume = {103},
},

@article{SP,
  author={Xianghong Zhou, Ming-Chih J. Kao, and Wing Hung Wong},
  title={Transitive functional annotation by shortest-path analysis of gene expression data},
  journal={PNAS},
  month={October},
  year={2002},
  volume={99},
  number={20},
  pages={12783-12788},
},
@article{GTA,
  author={Raji Balasubramanian, Thomas LaFramboise, Denise Scholtens, and Rober Gentleman},
  title={A graph-theoretic approach to testing associations between disparate sources of 
         functional genomics data},
  journal={Bioinformatics},
  year={2004},
  volume={20},
  number={18},
  pages={3353-3362},
},

@InCollection{WileyEncy,
 title = {Differential Expression with the Bioconductor Project},
 author = {A. von Heydebreck and W. Huber and R. Gentleman},
 year = {2004},
 booktitle= {Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics},
 publisher = {John Wiley and Sons},
}

@Article{Smyth2004,
  author =       {Smyth, Gordon K.},
  title =        {{Linear models and empirical Bayes methods for assessing differential expression in            
                 microarray experiments}},
  journal =      {Statistical Applications in Genetics and Molecular Biology},
  year =         {2004},
  volume =       {3},
  number =       {1},
  pages =        {article 3}
}


@article{FureyHaussler,
 title  = {Integration of the cytogenetic map with the draft human genome 
     sequence}, 
 author = {T. S. Furey and D. Haussler},
 journal = {Human Molecular Genetics}, 
 year = {2003}, 
 volume = {12}, 
 pages = {1037--1044},
 url = {DOI: 10.1093/hmg/ddg113}
}

@article{JiangGent2007,
author = {Z. Jiang and R. Gentleman},
title = {Extensions to Gene Set Enrichment},
journal = {Bioinformatics}, 
year = {2007},
volume = {23}, 
pages = {306--313}
}

@book{BiocCaseStudies,
  author = {F. Hahne and W. Huber and R. Gentleman and S. Falcon},
  title = {Bioconductor Case Studies},
  year = {2008},
  publisher = {Springer},
  address = {New York},
}


@article{Chiaretti2005,
  author =       {S. Chiaretti and X. Li and R. Gentleman and
                  A. Vitale and K. S. Wang and F. Mandelli and R. Foa
                  and J. Ritz},
  title =        {Gene Expression Profiles of B-lineage Adult Acute
                  Lymphocytic Leukemia Reveal Genetic Patterns that
                  Identify Lineage Derivation and Distinct Mechanisms
                  of Transformation},
  journal =      {Clinical Cancer Research},
  year =         {2005},
  volume =       {11},
  pages =        {7209-7219},
}


@ARTICLE{Caspersson1972,
author = { T Caspersson and  G Lomakka and  L Zech},
title = {The 24 fluorescence patterns of the human metaphase chromosomes -
      distinguishing characters and variability.},
journal = {Hereditas},
year = {1972},
volume = {67},
number = {1},
pages = {89-102}
}

@ARTICLE{Falcon-GOstats,
author = { S Falcon and  R Gentleman},
title = {Using {G}{O}stats to test gene lists for {G}{O} term association.},
journal = {Bioinformatics},
year = {2007},
volume = {23},
number = {2},
pages = {257-8}
}


@article{Simpson1982,
     title = {Simpson's Paradox in Real Life},
     author = {Wagner, Clifford H.},
     journal = {The American Statistician},
     volume = {36},
     number = {1},
     pages = {46--48},
     ISSN = {00031305},
     publisher = {American Statistical Association},
     year = {1982}
}


@incollection{limma,
    title = {Limma: linear models for microarray data},
    author = {Gordon K. Smyth},
    booktitle = {Bioinformatics and Computational Biology Solutions using R and Bioconductor},
    editor = {R. Gentleman and V. Carey and S. Dudoit and R. Irizarry and W. Huber},
    publisher = {Springer},
    address = {New York},
    year = {2005},
    pages = {397--420},
}
