@article{albertson03,
 author =   {D. G. Albertson and C. Collins and F McCormick and J. W. Gray},
 title =    {Chromosome aberrations in solid tumors},
 journal =      {Nat. Genet.},
 year =     {2003},
 OPTkey =   {},
 volume =   {34},
 OPTnumber =    {4},
 pages =    {369-76},
 OPTmonth =     {},
 OPTnote =      {},
 OPTannote =    {}
}

@PHDTHESIS{ambroise96,
   Author         = {C. Ambroise},
   School         = {Université Technique de Compiègne, France},
   Title          = {Approche probabiliste en classification automatique et contraintes de voisinage},
   Year           = {1996}
}

@INPROCEEDINGS{ambroise96b,
   Author         = {C. Ambroise},
   Booktitle      = {geoENV I- Geostatistics for Environmental Applications, Quantitative Geology and Geostatistics},
   Title          = {Clustering of spatial data by the {EM} algorithm},
   Year           = {1996}
}



@Article{autio03,
 author =   {Reija Autio and Sampsa Hautaniemi and Päivikki Kauraniemi and Olli Yli-Harja and Jaakko Astola and Maija Wolf and Anne Kallioniemi},
 title =    {{CGH-Plotter: MATLAB} toolbox for {CGH-data} analysis},
 journal =      {Bioinformatics},
 year =     {2003},
 OPTkey =   {},
 volume =   {19},
 OPTnumber =    {13},
 pages =    {1714-1715},
 OPTmonth =     {},
 OPTnote =      {},
 OPTannote =    {}
}



@Article{billerey01,
 author =   {C. Billerey and D. Chopin and M. H. Aubriot-Lorton and D. Ricol and S. Gil Diez de Medina and B. Van Rhijn and M. P. Bralet and M. A. Lefrere-Belda and J. B. Lahaye and C. C. Abbou and J. Bonaventure and E. S. Zafrani and T. van der Kwast and J. P. Thiery   and  F. Radvanyi},
 title =    {Frequent {FGFR3} mutations in papillary non-invasive bladder (p{T}a) tumors},
 journal =      {Am. J. Pathol.},
 year =     {2001},
 OPTkey =   {},
 volume =   {158},
 OPTnumber =    {},
 pages =    {955-1959},
 OPTmonth =     {},
 OPTnote =      {},
 OPTannote =    {}
}

@Article{burges98,
  author = {"Christopher J. C. Burges},
  title =  {A Tutorial on Support Vector Machines for Pattern Recognition},
  journal =    {Data Mining and Knowledge Discovery},
  volume = {2},
  number = {2},
  pages =  {121-167},
  year =   {1998}
}




@Article{cappellen97,
 author =   {D. Cappellen and S. Gil Diez de Medina and D. Chopin and J. P. Thiery and F. Radvanyi},
 title =    {Frequent loss of heterozygosity on chromosome 10q in muscle-invasive transitional cell carcinomas of the bladder},
 journal =      {Oncogene},
 year =     {1997},
 OPTkey =   {},
 volume =   {14},
 OPTnumber =    {25},
 pages =    {3059-66},
 OPTmonth =     {},
 OPTnote =      {},
 OPTannote =    {}
}

@INCOLLECTION{cleveland92,
   Author         = {W. S. Cleveland and E. Grosse and W. M. Shyu},
   Booktitle      = {Statistical Models in S},
   Title          = {Local regression models}
}



@Article{cleveland91,
 author =   {W. S. Cleveland and E. Grosse},
 title =    {Computational Methods for Local Regression},
 journal =      {Statistics and Computing},
 year =     {1991},
 OPTkey =   {},
 volume =   {1},
 OPTnumber =    {},
 pages =    {47-62},
 OPTmonth =     {},
 OPTnote =      {},
 OPTannote =    {}
}

@Article{cleveland88,
 author =   {W.S. Cleveland  and S.J. Devlin and E. and Grosse},
 title =    {Regression By Local Fitting},
 journal =      {Journal of Econometrics},
 year =     {1988},
 OPTkey =   {},
 volume =   {37},
 OPTnumber =    {},
 pages =    {87 -114},
 OPTmonth =     {},
 OPTnote =      {},
 OPTannote =    {}
}

@INCOLLECTION{dudoit03,
  AUTHOR = {S. Dudoit and Y. H. Yang},
  TITLE = {Bioconductor {R} packages for exploratory analysis and normalization of c{DNA} microarray data},
  BOOKTITLE = {The Analysis of Gene Expression Data: Methods and Software},
  PUBLISHER = {Springer, New York},
  YEAR = {2003},
  EDITOR = {G. Parmigiani and E. S. Garrett and R. A. Irizarry and S. L. Zeger},
}

@Article{fridlyand04,
 author =   {J. Fridlyand and A. Snijders and D. Pinkel and D. G.  Albertson  and A. N. Jain},
 title =    {Application of Hidden Markov Models to the analysis of the array {CGH} data},
 journal =      {Journal of Multivariate Analysis},
 year =     {2004},
 OPTkey =   {},
 OPTvolume =    {90},
 OPTnumber =    {},
 OPTpages =     {132-153},
 OPTmonth =     {},
 note =     {Special Issue on Multivariate Methods in Genomic Data Analysis},
 OPTannote =    {}
}


@Book{GenePix,
 author =   {{Axon Instruments}},
 ALTeditor =    {},
 title =    {GenePix Pro 5.0 User's Guide},
 publisher =    {\copyright Axon Instruments, Inc.},
 year =     {2003},
 OPTkey =   {},
 OPTvolume =    {},
 OPTnumber =    {},
 OPTseries =    {},
 OPTaddress =   {},
 OPTedition =   {},
 OPTmonth =     {},
 OPTnote =      {},
 OPTannote =    {}
}





@Article{guyon02,
 author =   {Isabelle Guyon and Jason Weston and Stephen Barnhill and Vladimir  Vapnik},
 title =    {Gene selection for cancer classification using support vector machines},
 journal =      {Mach. Learn.},
 year =     {2002},
 OPTkey =   {},
 OPTvolume =    {46},
 OPTnumber =    {},
 pages =    {389-422},
 OPTmonth =     {},
 OPTnote =      {},
 OPTannote =    {}
}




@Article{hanahan00,
 author =   {D. Hanahan and R. A. Weinberg},
 title =    {The hallmarks of cancer},
 journal =      {Cell},
 year =     {2000},
 OPTkey =   {},
 volume =   {100},
 number =   {1},
 pages =    {57-70},
 OPTmonth =     {},
 OPTnote =      {},
 OPTannote =    {}
}



@Article{hsu02,
 author =   {C. W. Hsu and C. J. Lin},
 title =    {A Comparison of Methods for Multi-class Support Vector Machines},
 journal =      {IEEE Transactions on Neural Networks},
 year =     {2002},
 OPTkey =   {},
 volume =   {13},
 OPTnumber =    {},
 pages =    {415-425},
 OPTmonth =     {},
 OPTnote =      {},
 OPTannote =    {}
}





@Article{ishkanian04,
 author =   {A. S. Ishkanian and C. A. Malloff and S. K. Watson and R. J. DeLeeuw and B. Chi and B. P. Coe and A. Snijders and D. G. Albertson and D. Pinkel and M. A. Marra and V. Ling and C. MacAulay and W. L. Lam},
 title =    {A tiling resolution {DNA} microarray with complete coverage of the human genome},
 journal =      {Nat. Genet.},
 year =     {2004},
 OPTkey =   {},
 volume =   {36},
 OPTnumber =    {3},
 pages =    {299-303},
 OPTmonth =     {},
 OPTnote =      {},
 OPTannote =    {}
}

@ARTICLE{jain02,
 Author         = {A. N. Jain and T. A. Tokuyasu and A. M. Snijders and R. Segraves and D. G. Albertson and D. Pinkel},
 Journal        = {Genome Res.},
 Pages          = {325--332},
 Title          = {Fully automatic quantification of microarray image data},
 Year           = {2002},
 volume         = {12},
 OPTnumber         = {2}
}



@InProceedings{jong03,
 author =  {Kees Jong and Elena Marchiori and Aad van der Vaart and Bauke Ylstra and Marjan Weiss and Gerrit Meijer},
 title =   {Chromosomal Breakpoint Detection in Human Cancer},
 booktitle =   {Applications of Evolutionary Computing, EvoWorkshops2003:
 Evo{BIO}, Evo{COP}, Evo{IASP}, Evo{MUSART}, Evo{ROB}, Evo{STIM}},
 year =    {2003},
 editor =  {G\"{u}nther R. Raidl and Stefano Cagnoni and
 Juan Jes\'{u}s Romero Cardalda and David W. Corne and Jens Gottlieb
 and Agn\`{e}s Guillot and Emma Hart and Colin G. Johnson and
 Elena Marchiori and Jean-Arcady Meyer and Martin Middendorf},
 volume =  {2611},
 series =  {LNCS},
 pages =   {54--65},
 address =     {University of Essex, England, UK},
 publisher_address =   {Berlin},
 month =   {14-16 April},
 organisation ={EvoNet},
 publisher =   {Springer-Verlag},
 note =    {},
 keywords =    {evolutionary computation, applications},
 ISBN =        {},
 url =         {},
 size =    {},
 abstract =    {},
 notes =   {EvoWorkshops2003},
}

@ARTICLE{koenker78,
   Author         = {R. W. Koenker and G. W. Bassett},
   Journal        = {Econometrica},
   Title          = {Regression quantiles},
   Year           = {1978}
}





@InProceedings{olshen03,
 author =   {Adam B. Olshen and E. S. Vankatraman},
 title =    {Change-point analysis or array-based comparative genomic hybridization data},
 OPTcrossref =  {},
 OPTkey =   {},
 booktitle = {Proceedings of the Joint Statistical Meetings, New York, August 11-15},
 OPTpages =     {},
 year =     {2002},
 OPTeditor =    {},
 OPTvolume =    {},
 OPTnumber =    {},
 OPTseries =    {},
 OPTaddress =   {},
 OPTmonth =     {},
 OPTorganization = {}
}



@ARTICLE{pinkel98,
   Author         = {D. Pinkel and R.  Segraves and D. Sudar and S. Clark and I.  Poole and D. Kowbel and C. Collins and W. L. Kuo and C. Chen and Y.  Zhai and S. H. Dairkee and B. M. Ljung and J. W.  Gray and D. G. Albertson},
   Journal        = {Nat. Genet.},
   Title          = {High resolution analysis of {DNA} copy number variation using comparative genomic hybridization to microarrays},
   Year           = {1998},
   volume     = {20},
   OPTnumber      = {},
   pages          = {207-211}
}



@ARTICLE{polzehl00,
   Author         = {J. Polzehl  and S. Spokoiny},
   Journal        = {J. Roy. Statistical Society, Series B},
   Title          = {Adaptive Weights Smoothing with applications to image restoration},
   Year           = {2000},
   pages          = {335-354}
}

@UNPUBLISHED{polzehl02,
   Author         = {J. Polzehl  and S. Spokoiny},
   Note           = {WIAS-Preprint 787},
   Title          = {Local likelihood modelling by adaptive weights smoothing},
   Year           = {2002}
}

@ARTICLE{R,
   Author         = {Ross Ihaka and Robert Gentleman},
   Journal        = {Journal of Computational and Graphical Statistics},
   Number         = {3},
   Pages          = {299--314},
   Title          = {R: A Language for Data Analysis and Graphics},
   Volume         = {5},
   Year           = {1996}
}

@Article{rakotomamonjy03,
 author =   {A. Rakotomamonjy},
 title =    {Variable Selection using SVM-based criteria},
 journal =      {Journal of Machine Learning Research},
 year =     {2003},
 OPTkey =   {},
 volume =   {3},
 OPTnumber =    {},
 pages =    {1357-1370},
 OPTmonth =     {},
 note =     {Special Issue on Variable Selection},
 OPTannote =    {}
}


@ARTICLE{Sen1975,
   Author         = {A. Sen and M. S. Srivastava},
   Journal        = {Ann. Statist.},
   Pages          = {98--108},
   Title          = {On tests for detecting a change in mean},
   Volume         = {3},
   Year           = {1975}
}

@ARTICLE{snijders01,
   Author         = {A. M. Snijders and N. Nowak and R. Segraves and S. Blackwood and N. Brown and J.  Conroy and G. Hamilton and A. K. Hindle and B.  Huey and K. Kimura and S. Law S and K. Myambo and J. Palmer and B. Ylstra and J. P. Yue and J. W. Gray and A. N. Jain and D. Pinkel and D. G. Albertson},
   Journal        = {Nat. Genet.},
   Title          = {Assembly of microarrays for genome-wide measurement of {DNA} copy number},
   Year           = {2001},
   volume         = {29},
   OPTnumber         = {3},
   pages          = {263-4}
}





@Article{sobin97,
 author =   {L. H. Sobin  and I. D. Fleming},
 title =    {{TNM} Classification of Malignant Tumors, fifth edition. Union Internationale Contre le Cancer and the American Joint Committee on Cancer},
 journal =      {Cancer},
 year =     {1997},
 OPTkey =   {},
 volume =   {80},
 OPTnumber =    {9},
 pages =    {1803-04},
 OPTmonth =     {},
 OPTnote =      {},
 OPTannote =    {}
}

@Article{solinas97,
 author =   {S. Solinas-Toldo and S. Lampel and S. Stilgenbauer and J. Nickolenko and A. Benner and H. Dohner and T. Cremer and P. Lichter},
 title =    {Matrix-based comparative genomic hybridization: Biochips to screen for genomic imbalances},
 journal =      {Genes Chromosomes Cancer},
 year =     {1997},
 OPTkey =   {},
 volume =   {20},
 OPTnumber =    {4},
 pages =    {399-407},
 OPTmonth =     {},
 OPTnote =      {},
 OPTannote =    {}
}



@Article{vogelstein89,
 author =   {B. Vogelstein and E. R. Fearon and S. E. Kern and S. R. Hamilton and A. C. Preisinger and Y. Nakamura and R. White},
 title =    {Allelotype of colorectal carcinomas},
 journal =      {Science},
 year =     {1989},
 OPTkey =   {},
 volume =   {244},
 OPTnumber =    {4901},
 pages =    {207-11},
 OPTmonth =     {},
 OPTnote =      {},
 OPTannote =    {}
}

@ARTICLE{Yang01,
   Author         = {Y. H. Yang and S. Dudoit and T. Speed},
   Note           = {SPIE BiOS 2001, San Jose, California, January 2001},
   Title          = {Normalization for c{DNA} microarray data},
   Year           = {2001}
}

@ARTICLE{Workman02,
   Author         = {C. Workman and L. J. Jensen and H. Jarmer and R. Berka and L. Gautier and H. B. Nielsen and H. H. Saxild and C. Nielsen and S. Brunak and S. Knidsen},
   Journal        = {Genome Biology},
   Title          = {A new non-linear normalization method for reducing variability in {DNA} microarray experiments},
   Year           = {2002}
}

@ARTICLE{Baird04,
   Author         = {D. Baird and P. Johnstone and T. Wilson},
   Journal        = {Bioinformatics},
   Title          = {Normalization of Microarray Data Using a Spatial Mixed Model analysis which includes Splines},
   Year           = {2004},
   Volume         = {20},
   Pages          = {3196-3205}
}

@ARTICLE{Yang02,
   Author         = {Y. H. Yang  and S. Dudoit and P. Luu and D. M. Lin and V. Pend and J. Ngai and T. P. Speed},
   Journal        = {Nucleic Acids Research},
   Title          = {Normalization of cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation},
   Year           = {2002},
   volume         = {30},
   pages          = {e15:1-e15:11}
}

@ARTICLE{phupe04,
   Author         = {P. Hupé and N. Stransky and J-P. Thiery and F. Radvanyi and E. Barillot},
   Journal        = {Bioinformatics},
   Title          = {Analysis of array {CGH} data: from signal ratios to gain and loss of {DNA} regions},
   Year           = {2004},
   volume         = {20},
   pages          = {3413 - 3422}
}

@ARTICLE{Pollack02,
   Author         = {J. R. Pollack and T. Sorlie and C. M. Perou and . A. Rees and S. S. Jeffreys and P.E. Lonning and R. Tibshirani and D. Botstein and A-L. Borresen-Dale and P. O. Brown},
   Journal        = {PNAS},
   Year           = {2002},
   Title          = {Microarray analysis reveals a direct role of {DNA} copy number alteration in the transcriptional program of breast tumors}
}

@ARTICLE{Wang04,
   Author         = {J. Wang and L. A. Meza-Zepeda, S. H. Kresse and O. Myklebost},
   Journal        = {BMC Bioinformatics},
   Year           = {2004},
   Title          = {{M-CGH}: Analysing microarray-based {CGH} experiments},
   Volume         = {5},
   Pages          = {74}
}

@ARTICLE{NeuvialHupeBarillot06,
  author = {Neuvial, P. and Hupé, P. and Brito, I. and Liva, S. and Manié, E. and
	Brennetot, C. and Radvanyi, F. and Aurias, A. and Barillot, E.},
  title = {Spatial normalization of array-{CGH} data.},
  journal = {BMC Bioinformatics},
  year = {2006},
  volume = {7},
  pages = {264},
  number = {1},
  month = {May},
  doi = {10.1186/1471-2105-7-264},
  keywords = {16716215},
  pii = {1471-2105-7-264},
  pmid = {16716215},
  url = {http://dx.doi.org/10.1186/1471-2105-7-264},
}

@Manual{R,
     title        = {R: A language and environment for
                     statistical computing},
     author       = {{R Development Core Team}},
     organization = {R Foundation for Statistical Computing},
     address      = {Vienna, Austria},
     year         = 2004,
     note         = {ISBN 3-900051-00-3},
     url          = {http://www.R-project.org}
   }