@Manual{haar-package,
    title = {HaarSeg: HaarSeg},
    author = {Erez Ben-Yaacov and Yonina C. Eldar},
    year = {2009},
    note = {R package version 0.0.3/r4},
    url = {http://R-Forge.R-project.org/projects/haarseg/},
  }

@Manual{Rcitation,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Core Team}},
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@article{Rueda2010a,
author = {Rueda, Oscar M and Diaz-Uriarte, Ramon},
journal = {Current Bioinformatics},
keywords = {acgh,common regions,copy number alterations,recurrent},
pages = {1--17},
title = {{Finding Recurrent Copy Number Alteration Regions : A Review of Methods}},
volume = {5},
year = {2010}
}

@article{VandeWiel2007,
author = {van de Wiel, Mark A and van Wieringen, Wessel N},
issn = {1176-9351},
journal = {Cancer informatics},
keywords = {array cgh,dimension reduction,fdr,statistical testing,tumor profiles},
month = jan,
number = {0},
pages = {55--63},
pmid = {19455235},
title = {{CGHregions: Dimension Reduction for Array CGH Data with Minimal Information Loss.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2675846\&tool=pmcentrez\&rendertype=abstract},
volume = {3},
year = {2007}
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  @Manual{aCGHpackage,
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    author = {Jane Fridlyand and Peter Dimitrov},
    year = {2010},
    note = {R package version 1.41.2},
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  @Manual{snapCGH,
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    year = {2009},
    note = {R package version 1.33.0},
  }


@article{hmm-fridlyand,
author = {Fridlyand, Jane   and Snijders, Antoine  M.  and Pinkel, Dan   and
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journal = {Journal of Multivariate Analysis},
pages = {132--153},
title = {{Hidden Markov models approach to the analysis of array CGH data. }},
volume = {90},
year = {2004}
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@Manual{CGHregions-manual,
    title = {CGHregions: Dimension Reduction for Array CGH Data with Minimal Information Loss.},
    author = {Vosse, Sjoerd and van de Wiel, Mark},
    year = {2009},
    note = {R package version 1.7.1},
  }

@article{Diaz-Uriarte2007,
author = {Diaz-Uriarte, Ramon and Rueda, Oscar M},
doi = {10.1371/journal.pone.0000737},
issn = {1932-6203},
journal = {PloS one},
month = jan,
number = {1},
pages = {e737},
pmid = {17710137},
title = {{ADaCGH: A parallelized web-based application and R package for the analysis of aCGH data.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1940324\&tool=pmcentrez\&rendertype=abstract},
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year = {2007}
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@article{Carro2010,
author = {Carro, Angel and Rico, Daniel and Rueda, Oscar M and Diaz-Uriarte, Ramon and Pisano, David G},
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issn = {1362-4962},
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pages = {W182--7},
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url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2896163\&tool=pmcentrez\&rendertype=abstract},
volume = {38 Suppl},
year = {2010}
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@article{waves-hsu,
author = {Hsu, L and Self, S G and Grove, D and Randolph, T and Wang, K and Delrow, J J and Loo, L and Porter, P},
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journal = {Biostatistics},
month = apr,
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pages = {211--226},
title = {{Denoising array-based comparative genomic hybridization data using wavelets.}},
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year = {2005}
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@article{biohmm,
author = {Marioni, J C and Thorne, N P and Tavar\'{e}, S},
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month = may,
number = {9},
pages = {1144--1146},
title = {{BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data.}},
url = {http://view.ncbi.nlm.nih.gov/pubmed/16533818},
volume = {22},
year = {2006}
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@article{haarseg-paper,
author = {Ben-Yaacov, E and Eldar, Y C},
doi = {10.1093/bioinformatics/btn272},
issn = {1460-2059},
journal = {Bioinformatics (Oxford, England)},
month = aug,
number = {16},
pages = {i139--i145},
title = {{A fast and flexible method for the segmentation of aCGH data.}},
url = {http://dx.doi.org/10.1093/bioinformatics/btn272},
volume = {24},
year = {2008}
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@article{cghseg,
author = {Picard, F and Robin, S and Lavielle, M and Vaisse, C and Daudin, J J},
doi = {10.1186/1471-2105-6-27},
issn = {1471-2105},
journal = {BMC Bioinformatics},
title = {{A statistical approach for array CGH data analysis.}},
url = {http://dx.doi.org/10.1186/1471-2105-6-27},
volume = {6},
year = {2005}
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@Article{glad-paper,
author = {Hupe, P.  and Stransky, N.  and Thiery, J. P.  and Radvanyi, F.  and
Barillot, E.},
title = {Analysis of array CGH data: from signal ratio to
gain and loss of DNA regions.},
journal = {Bioinformatics},
year = {2004},
pages = {3413--3422},
}


@Article{tilingarray,
    author = {Wolfgang Huber and Joern Toedling and Lars M. Steinmetz},
    title = {Transcript mapping with high-density oligonucleotide tiling arrays},
    journal = {Bioinformatics},
    year = {2006},
    volume = {22},
    pages = {1963-1970},
  }


@article{CBS-paper,
author = {Venkatraman, E S and Olshen, Adam B},
doi = {10.1093/bioinformatics/btl646},
issn = {1367-4811},
journal = {Bioinformatics (Oxford, England)},
month = mar,
number = {6},
pages = {657--663},
title = {{A faster circular binary segmentation algorithm for the analysis of array CGH data.}},
url = {http://dx.doi.org/10.1093/bioinformatics/btl646},
volume = {23},
year = {2007}
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  @Manual{glad-package,
    title = {GLAD: Gain and Loss Analysis of DNA},
    author = {Philippe Hupe},
    year = {2011},
    note = {R package version 2.27.0},
    url = {http://bioinfo.curie.fr},
  }



