@article{langfelder2008wgcna,
  title={WGCNA: an R package for weighted correlation network analysis},
  author={Langfelder, Peter and Horvath, Steve},
  journal={BMC bioinformatics},
  volume={9},
  number={1},
  pages={559},
  year={2008},
  publisher={BioMed Central}
}

 @Manual{RProject,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Development Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2008},
    note = {{ISBN} 3-900051-07-0},
    url = {http://www.R-project.org},
  }

@article{YunqiWu2016,
  title={Quantitative proteomic analysis of two different rice varieties reveals that drought tolerance is correlated with reduced abundance of photosynthetic machinery and increased abundance of ClpD1 protease},
  author={Wu, Yunqi and Mirzaei, Mehdi and Pascovici, Dana and Chick, Joel M and Atwell, Brian J and Haynes, Paul A},
  journal={Journal of proteomics},
  volume={143},
  pages={73--82},
  year={2016},
  publisher={Elsevier}
}

@article{pascovici2012plogo,
  title={PloGO: Plotting gene ontology annotation and abundance in multi-condition proteomics experiments},
  author={Pascovici, Dana and Keighley, Tim and Mirzaei, Mehdi and Haynes, Paul A and Cooke, Brett},
  journal={Proteomics},
  volume={12},
  number={3},
  pages={406--410},
  year={2012},
  publisher={Wiley Online Library}
}

  @ARTICLE {SimonMADesign,
    title = {Design of Studies Using DNA Microarrays},
    author = {Simon, Richard and Radmacher, Michael D. and Dobbin, Kevin},
    year = {2002},
    journal = {Genetic Epidemiology},
    volume = {23},
    pages = {21-36},
  }

  @ARTICLE {SpeedMADesign,
    title = {Design Issues for cDNA Microarray Experiments},
    author = {Yang, Hwa, Yee and Speed, Terry},
    year = {2002},
    journal = {Nature Reviews},
    volume = {3},
    pages = {579-588},
  }

 @ARTICLE {ZybailovNSAF,
    title = {Statistical Analysis of Membrane Proteome Expression Changes in Saccharomyces cerevisiae},
    author = {Zybailov, Boris and Moseley, Amber D. and Sardiu, Mihaela E.
            and Coleman, Michael K. and Florens, Laurence and Washburn, Michael P.},
    year = {2006},
    journal = {Journal of Proteome Research},
    volume = {5},
    number = {9},
    pages = {2339-2347},
  }

   @Book{ChambersStatMod,
    title = {Statistical Models in S},
    editor = {Chambers, J. M. and Hastie, T. J.},
    publisher = {Wadsworth and Brooks/Cole},
    year = {1992}
  }

   @Book{ChambersGraphicalDataAn,
    title = {Graphical Methods for Data Analysis},
    author = {Chambers, J. M. and  Cleveland, W.S. and Kleiner, B. and Tukey, P.A.},
    publisher = {Wadsworth and Brooks/Cole},
    year = {1983}
  }


   @ARTICLE {PavelkaPLGEMMA,
    author = {Pavelka N and Pelizzola M and Vizzardelli C and Capozzoli M and Splendiani A and Granucci F and Ricciardi-Castagnoli P},
    title = {A power law global error model for the identification of differentially expressed genes in microarray data},
    journal = {BMC Bioinformatics},
    volume = {5},
    year = {2004},
    pages = {203},
    doi = {http://dx.doi.org/10.1186/1471-2105-5-203},
    publisher = {BioMed Central},
  }


    @ARTICLE {PavelkaPLGEM,
    title = {Statistical similarities between transcriptomics and quantitative shotgun proteomics data},
    author = {Pavelka, N. and Fournier, M. L. and Swanson, S. K. and Pelizzola, M. and
         Ricciardi-Castagnoli, P. and Florens, L. and Washburn, M. P.},
    year = {2008},
    journal = {Mol Cell Proteomics},
    volume = {7},
    pages = {631-644}
  }


  @INCOLLECTION{MurtaghHclust,
   author = "Murtagh, F",
   title = "Multidimensional Clustering Algorithms",
   booktitle = "COMPSTAT Lectures 4",
   publisher = "Wuerzburgh: Physica-Verlag",
   year = 1985,
}


  @INCOLLECTION{GentlemanBioinfR,
   editor = {Gentleman, R and Irizarry, R. A. and Carey, V.J. and Dudoit S. and Huber W.},
   author = {Huber, W and Li X. and Gentleman, R.},
   title = "Visualizing Data",
   booktitle = "Bioinformatics and Computational Biology Solutions Using R and Bioconductor",
   publisher = "Springer",
   pages = {161},
   year = 2005,
}

@ARTICLE {Chick,
    title = {A combination of Immobilized pH Gradients Improves Membrane Proteomics},
    author = {Chick, J.M. and Haynes, P.A. and Bjellqvist, B. and Baker, M.S.},
    year = {xxxx},
    journal = {Journal of Proteome Research},
    volume = {x},
    pages = {xx}
  }

@ARTICLE {Gammulla,
   title = { Differential metabolic response of cultured rice (Oryza sativa) cells exposed to high- and low-temperature stress },
   author = {Gammulla, C. G. and Pascovici, D. and Atwell, B. J. and Haynes, P. A.},
   year = { 2010 },
   journal = { Proteomics }, 
   doi = { http://dx.doi.org/10.1002/pmic.201000054 },
   publisher = { WILEY-VCH Verlag }
}


@Article{GentlemanLang,
author = {R. Gentleman and D. {Temple Lang}},
title = {Statistical Analyses and Reproducible Research},
publisher = {Submitted},
year = {2003}
}


@INPROCEEDINGS{Leisch2002,
  AUTHOR = {Friedrich Leisch},
  TITLE = {Sweave: Dynamic Generation of Statistical Reports Using
		  Literate Data Analysis},
  BOOKTITLE = {Compstat 2002 --- Proceedings in Computational
		  Statistics},
  PAGES = {575--580},
  YEAR = 2002,
  EDITOR = {Wolfgang H{\"a}rdle and Bernd R{\"o}nz},
  PUBLISHER = {Physika Verlag, Heidelberg, Germany},
  NOTE = {ISBN 3-7908-1517-9},
  URL = {http://www.ci.tuwien.ac.at/~leisch/Sweave}
}



@ARTICLE {PengRR2009, 
	title = {Reproducible reasearch and Biostatistics},
	author = { Peng, Roger D.},
	year = {2009},
	journal = "Biostatistics",
	doi = {10.1093/biostatistics/kxp014},
	volume = {10},
	number = {3},
	pages = {405-408}
}


@ARTICLE {BiostatEdit2010,
	title = {Editorial},
	author = { Diggle, Peter J. and Zeger, Scott L. },
	year = {2010},
	journal = {Biostatistics},
	doi = { 10.1093/biostatistics/kxq029},
	volume = {11},
	number = {3},
	pages = {3}
}

@inproceedings{Wavelab,
author= {J. Buckheit and D. L. Donoho},
title = {Wavelab and reproducible research},
booktitle ={ Wavelets and Statistics},
editor ={ A. Antoniadis},
publisher = {Springer-Verlag},
year = {1995}
}


@article{XTandem,
author = {Robertson Craig and Ronald C. Beavis},
title={ TANDEM: matching proteins with mass spectra},
journal={Bioinformatics},
year={2004},
volume={20},
pages={1466-7}
}


@Manual{biomaRt,
title = {biomaRt: Interface to BioMart databases (e.g. Ensembl, Wormbase and Gramene)},
author = {Steffen Durinck and Wolfgang Huber and Sean Davis},
year = {},
note = {R package version 2.2.0}
  }

@ARTICLE{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{Mirzaei,
    author = {M Mirzaei and D Pascovici and B Atwell and P Haynes},
    title = {Differential Regulation of Aqualporins and Small GTPases proteins in rice leaves subjected to drought stress and recovery},
    journal = {Under review}
  }


@ARTICLE{WEGO,
author={Jia Ye and Lin Fang and Hongkun Zheng and Yong Zhang and Jie Chen and Zengjin Zhang and Jing Wang and Shengting Li and Ruiqiang Li and Lars Bolund and Jun Wang},
title={WEGO: a web tool for plotting GO annotations},
journal={Nucleic Acids Research},
year={2006},
volume={34},
pages={W293-W297},
note={Web Server Issue}
}



@ARTICLE {AgBase,
	title = {AgBase: a functional genomics resource for agriculture},
	author = { McCarthy, F. and Wang, N. and Magee, G. B. and Nanduri, B. and Lawrence, M. and Camon, E. and Barrell, D. and Hill, D. and Dolan, M. and Williams, W. P. and Luthe, D. and Bridges, S. and Burgess, S.},
	year = {2006},
	journal = {BMC Genomics},
	doi = { 10.1186/1471-2164-7-229 },
	volume = {7},
	number = {1},
	pages = {229},
	url = { http://www.biomedcentral.com/1471-2164/7/229 },
}




































