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@Misc{RedeR,
    title = {{RedeR}: bridging the gap between network analysis and visualization. },
    author = {Mauro Antonio Alves Castro and Xin Wang and Florian Markowetz.},
    organization = {Cancer Research UK - Cambridge Research Institute, Cambridge University. },
    address = {Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK. },
    year = {2011},
    type = {R package},
    url = {http://www.markowetzlab.org/software/networks.html},
    }

@Manual{XMLRPC,
    title = {XMLRPC: Remote Procedure Call (RPC) via XML in R},
    author = {Duncan Temple Lang},
    year = {2010},
    note = {R package},
    url = {http://www.omegahat.org/XMLRPC}
    }

@Manual{rJava,
    title = { rJava: Low-level R to Java interface},
    author = {Simon Urbanek},
    year = {2010},
    note = {R package},
    url = {http://CRAN.R-project.org/package=rJava}
    }
  
@Article{igraph,
    title = {The igraph software package for complex network research},
    author = {Gabor Csardi and Tamas Nepusz},
    journal = {InterJournal},
    volume = {Complex Systems},
    pages = {1695},
    year = {2006},
    url = {http://igraph.sf.net},
    }

@Article{Curtis2012,
    title = {The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups},
    author = {Christina Curtis et al},
    journal = {Nature},
    volume = {486},
    pages = {346-352},
    year = {2012},
    doi = {10.1038/nature10983}
    }

@Manual{JavaGD,
    title = {JavaGD: Java Graphics Device},
    author = {Simon Urbanek},
    year = {2010},
    note = {R package},
    url = {http://CRAN.R-project.org/package=JavaGD},
    }
  
@Manual{Rcore,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2012},
    note = {{ISBN} 3-900051-07-0},
    url = {http://www.R-project.org/},
    }

@Article{Gentleman2004,
  AUTHOR = {Gentleman, Robert and Carey, Vincent and Bates, Douglas and Bolstad, Ben and Dettling, Marcel and Dudoit, Sandrine and Ellis, Byron and Gautier, Laurent and Ge, Yongchao and Gentry, Jeff and Hornik, Kurt and Hothorn, Torsten and Huber, Wolfgang and Iacus, Stefano and Irizarry, Rafael and Leisch, Friedrich and Li, Cheng and Maechler, Martin and Rossini, Anthony and Sawitzki, Gunther and Smith, Colin and Smyth, Gordon and Tierney, Luke and Yang, Jean and Zhang, Jianhua},
  TITLE = {Bioconductor: open software development for computational biology and bioinformatics},
  JOURNAL = {Genome Biology},
  VOLUME = {5},
  YEAR = {2004},
  NUMBER = {10},
  PAGES = {R80},
  URL = {http://genomebiology.com/2004/5/10/R80},
  DOI = {10.1186/gb-2004-5-10-r80},
  PubMedID = {15461798},
  ISSN = {1465-6906},
  }

@article{Subramanian2005,
  author = {Subramanian, Aravind and Tamayo, Pablo and Mootha, Vamsi K. and Mukherjee, Sayan and Ebert, Benjamin L. and Gillette, Michael A. and Paulovich, Amanda and Pomeroy, Scott L. and Golub, Todd R. and Lander, Eric S. and Mesirov, Jill P.}, 
  title = {Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles}, 
  volume = {102}, 
  number = {43}, 
  pages = {15545-15550}, 
  year = {2005}, 
  doi = {10.1073/pnas.0506580102}, 
  URL = {http://www.pnas.org/content/102/43/15545.abstract}, 
  eprint = {http://www.pnas.org/content/102/43/15545.full.pdf+html}, 
  journal = {Proceedings of the National Academy of Sciences of the United States of America}, 
  }

@Article{Castro2012,
  author = {Mauro AA Castro and Xin Wang and Michael NC Fletcher and Kerstin B Meyer and Florian Markowetz},
  title = {{RedeR}: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations.},
  journal = {Genome Biology},
  year = {2012},
  volume = {13},
  pages = {R29},
  number = {4},
  }

@Article{Fletcher2013,
  author = {Michael NC Fletcher and Mauro AA Castro and Suet-Feung Chin and Oscar Rueda and Xin Wang and Carlos Caldas and Bruce AJ Ponder and Florian Markowetz and Kerstin B Meyer},
  title = {Master regulators of {FGFR2} signalling and breast cancer risk.},
  journal = {Nature Communications},
  year = {2013},
  volume = {4},
  pages = {2464}
  }

@article{Wang2011,
author = {Wang, Xin and Terfve, Camille and Rose, John C. and Markowetz, Florian}, 
title = {HTSanalyzeR: an {R}/Bioconductor package for integrated network analysis of high-throughput screens}, 
volume = {27}, 
number = {6}, 
pages = {879-880}, 
year = {2011}, 
doi = {10.1093/bioinformatics/btr028}, 
URL = {http://bioinformatics.oxfordjournals.org/content/27/6/879.abstract}, 
eprint = {http://bioinformatics.oxfordjournals.org/content/27/6/879.full.pdf+html}, 
journal = {Bioinformatics} 
}

@Article{Margolin2006a,
AUTHOR = {Margolin, Adam and Nemenman, Ilya and Basso, Katia and Wiggins, Chris and Stolovitzky, Gustavo and Favera, Riccardo and Califano, Andrea},
TITLE = {{ARACNE}: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context},
JOURNAL = {BMC Bioinformatics},
VOLUME = {7},
YEAR = {2006},
NUMBER = {Suppl 1},
PAGES = {S7},
DOI = {10.1186/1471-2105-7-S1-S7},
PubMedID = {16723010},
ISSN = {1471-2105},
}

@article{Margolin2006b,
  Annote = {10.1038/nprot.2006.106},
	Author = {Margolin, Adam A and Wang, Kai and Lim, Wei Keat and Kustagi, Manjunath and Nemenman, Ilya and Califano, Andrea},
	Date = {2006/07//print},
	Date-Added = {2012-10-16 00:26:25 +0000},
	Date-Modified = {2012-10-16 00:26:25 +0000},
	Isbn = {1754-2189},
	Journal = {Nat. Protocols},
	L3 = {http://www.nature.com/nprot/journal/v1/n2/suppinfo/nprot.2006.106_S1.html},
	M3 = {10.1038/nprot.2006.106},
	Month = {07},
	Number = {2},
	Pages = {662--671},
	Publisher = {Nature Publishing Group},
	Title = {Reverse engineering cellular networks},
	Ty = {JOUR},
	Url = {http://dx.doi.org/10.1038/nprot.2006.106},
	Volume = {1},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nprot.2006.106},
  }

@Article{Meyer2008,
  AUTHOR = {Meyer, Patrick and Lafitte, Frederic and Bontempi, Gianluca},
  TITLE = {minet: A {R}/Bioconductor package for Inferring Large Transcriptional Networks Using Mutual Information},
  JOURNAL = {BMC Bioinformatics},
  VOLUME = {9},
  YEAR = {2008},
  NUMBER = {1},
  PAGES = {461},
  URL = {http://www.biomedcentral.com/1471-2105/9/461},
  DOI = {10.1186/1471-2105-9-461},
  PubMedID = {18959772},
  ISSN = {1471-2105},
  }

@article{Lefebvre2010,
  Annote = {10.1038/msb.2010.31},
	Author = {Lefebvre, Celine and Rajbhandari, Presha and Alvarez, Mariano J and Bandaru, Pradeep and Lim, Wei Keat and Sato, Mai and Wang, Kai and Sumazin, Pavel and Kustagi, Manjunath and Bisikirska, Brygida C and Basso, Katia and Beltrao, Pedro and Krogan, Nevan and Gautier, Jean and Dalla-Favera, Riccardo and Califano, Andrea},
	Date = {2010/06/08/print},
	Date-Added = {2012-10-16 00:49:14 +0000},
	Date-Modified = {2012-10-16 00:49:14 +0000},
	Day = {08},
	Journal = {Mol Syst Biol},
	L3 = {http://www.nature.com/msb/journal/v6/n1/suppinfo/msb201031_S1.html},
	M3 = {10.1038/msb.2010.31},
	Month = {06},
	Publisher = {EMBO and Macmillan Publishers Limited},
	Title = {A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers},
	Ty = {JOUR},
	Url = {http://dx.doi.org/10.1038/msb.2010.31},
	Volume = {6},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/msb.2010.31}
  }

@article{Carro2010,
  Annote = {10.1038/nature08712},
  	Author = {Carro, Maria S and Lim, Wei K and Alvarez, Mariano J and Bollo, Robert J and Zhao, Xudong and Snyder, Evan Y and Sulman, Erik P and Anne, Sandrine L and Doetsch, Fiona and Colman, Howard and Lasorella, Anna and Aldape, Ken and Califano, Andrea and Iavarone, Antonio},
	Date = {2010/01/21/print},
	Date-Added = {2012-10-16 01:47:39 +0000},
	Date-Modified = {2012-10-16 01:47:39 +0000},
	Day = {21},
	Isbn = {0028-0836},
	Journal = {Nature},
	L3 = {http://www.nature.com/nature/journal/v463/n7279/suppinfo/nature08712_S1.html},
	M3 = {10.1038/nature08712},
	Month = {01},
	Number = {7279},
	Pages = {318--325},
	Publisher = {Macmillan Publishers Limited. All rights reserved},
	Title = {The transcriptional network for mesenchymal transformation of brain tumours},
	Ty = {JOUR},
	Url = {http://dx.doi.org/10.1038/nature08712},
	Volume = {463},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature08712}}


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