%
%  $Description: Sample bibliography$
%
%  $Author: dimitrov $ 
%  $Date: 2004/05/07 23:59:17 $
%  $Revision: 1.5 $
%
@string{JASA= {Journal of the American Statistical Association}}
@string{PNAS = {Proc. Natl. Acad. Sci.}}

@Article{Snijdersetal01,
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 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},
title =        {Assembly of microarrays for genome-wide measurement of DNA copy number},
journal =   {Nature Genetics},
year =         {2001},
OPTkey =       {},
volume =    {29},
OPTnumber =    {},
OPTpages =     {},
month =     {November},
OPTnote =         {},
OPTannote =    {}
}


@Article{Snijdersetal03,
author =       {A. M. Snijders and J. Fridlyand and D. Mans and R. Segraves and A. N. Jain and D. Pinkel and D. G. Albertson},
title =        {Shaping of tumors and drug-resitant genomes by instability and selection},
journal =   {Oncogene},
year =         {2003},
OPTkey =       {},
OPTvolume =    {},
OPTnumber =    {},
OPTpages =     {},
OPTmonth =     {},
note =         {(in press)},
OPTannote =    {}
}

@InProceedings{OlshenandVenkatraman02,
author =       {A. B. Olshen and E. S. Venkatraman},
title =        {Change-point analysis of array-based comparative genomic hybridization data},
booktitle =    {Proceedings of the Joint Statistical Meetings},
OPTcrossref =  {},
OPTkey =       {},
pages =     {2530--2535},
year =         {2002},
OPTeditor =    {},
OPTvolume =    {},
OPTnumber =    {},
OPTseries =    {},
OPTaddress =   {},
OPTmonth =     {},
OPTorganization = {},
OPTpublisher = {},
OPTnote =      {},
OPTannote =    {}
}


@InCollection{Jongetal2002,
author = 	 {K. Jong and E. Marchiori and A. van der Vaart and B. Ylstra and G. Meijer and M. Weiss},
title = 	 {Chromosomal breakpoint detection in array comparative genomic hybridization data},
booktitle = 	 {In Applications of evolutionary computing: Evolutionary computation and bioinformatics},
OPTcrossref =  {},
OPTkey = 	 {},
pages = 	 {54--65},
publisher = {Springer},
year = 	 {2003},
OPTeditor = 	 {},
volume = 	 {2611},
OPTnumber = 	 {},
OPTseries = 	 {},
OPTtype = 	 {},
OPTchapter = 	 {},
OPTaddress = 	 {},
OPTedition = 	 {},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@InProceedings{Rabiner89,
author =       {L. R. Rabiner},
title =        {A Tutorial on hidden Markov Models and selected applications in speech recognition},
booktitle =    {Proceedings of the IEEE},
OPTcrossref =  {},
OPTkey =       {},
pages =     {257--285},
year =         {1989},
OPTeditor =    {},
volume =    {77},
number =    {},
OPTseries =    {},
OPTaddress =   {},
month =     {February},
OPTorganization = {},
OPTpublisher = {},
OPTnote =      {},
OPTannote =    {}
}


@Article{R,
author =       {R. Ihaka and R. Gentleman},
title =        {R: A Language for Data Analysis and Graphics},
journal =      {Journal of Computational and Graphical Statistics},
year =         {1996},
OPTkey =       {},
volume =       {5},
OPTnumber =    {},
pages =        {299--314},
OPTmonth =     {},
OPTnote =      {},
OPTannote =    {}
}

@Book{Kaufman&Rousseeuw,
author =       {L. Kaufman and P. J. Rousseeuw},
ALTeditor =    {},
title =        {Finding Groups in Data: An Introduction to Cluster Analysis},
publisher =    {Wiley, New York.},
year =         {1990},
OPTkey =       {},
OPTvolume =    {},
OPTnumber =    {},
OPTseries =    {},
OPTaddress =   {},
OPTedition =   {},
OPTmonth =     {},
OPTnote =      {},
OPTannote =    {}
}


@InCollection{Akaike,
author = 	 {H. Akaike},
title = 	 {Fitting autoregressive models for prediction},
booktitle = 	 {Annals of the Institute of Statistical Mathematics},
OPTcrossref =  {},
OPTkey = 	 {},
pages = 	 {243--247},
publisher = {Kluwer Academic Publishers},
year = 	 {1969},
OPTeditor = 	 {},
OPTvolume = 	 {21},
OPTnumber = 	 {},
OPTseries = 	 {},
OPTtype = 	 {},
OPTchapter = 	 {},
OPTaddress = 	 {},
OPTedition = 	 {},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Article{Schwarz,
author = 	 {G. Schwarz},
title = 	 {Estimating the dimension of a model},
journal = 	 {The Annals of Statistics},
year = 	 {1978},
OPTkey = 	 {},
OPTvolume = 	 {6},
OPTnumber = 	 {},
OPTpages = 	 {461--464},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}


@Article{Loeb01,
author =       {L. A. Loeb},
title =        {A mutator phenotype in cancer},
journal =   {Cancer Research},
year =         {2001},
OPTkey =       {},
volume =    {61},
OPTnumber =    {},
pages =     {3230--3239},
OPTmonth =     {},
OPTnote =         {},
OPTannote =    {}
}

@Article{Albertson03,
author =       {D. G. Albertson},
title =        {Profiling breast cancer by array CGH},
journal =   {Breast Cancer Research Treat.},
year =         {2003},
OPTkey =       {},
volume =    {78},
OPTnumber =    {},
pages =     {289--298},
month =     {April},
note =         {(in press)},
OPTannote =    {}
}


@Article{Waldmanetal00,
author =       {F. M. Waldman and S. DeVries and K. L. Chew and D. H. Moore and K. Kerlikowske and B. M. Ljung},
title =        {Chromosomal alterations in ductal carcinomas in situ and their in situ recurrences},
journal =   {Journal of National Cancer Institute},
year =         {2000},
OPTkey =       {},
volume =    {92},
OPTnumber =    {},
pages =     {313-320},
OPTmonth =     {November},
OPTnote =         {},
OPTannote =    {}
}

@Article{Yangetal02,
author =       {Y. H. Yang and S. Dudoit and P. Luu and D. M. Lin and V. Peng and J. Ngai and T. P. Speed},
title =        {Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation},
journal =   {Nucleic Acids Research},
year =         {2002},
OPTkey =       {},
volume =    {30},
OPTnumber =    {},
OPTpages =     {},
month =     {February},
OPTnote =         {},
OPTannote =    {}
}

@Article{Bockeretal99,
author =       {T. Bocker and J. Ruschoff and R. Fishel},
title =        {Molecular diagnostics of cancer predisposition: hereditary non-polyposis colorectal carcinoma and mismatch repair defects.}, 
journal =   {Biochim Biophys Acta},
year =         {1999},
OPTkey =       {},
volume =    {1423},
number =    {3},
OPTpages =     {},
OPTmonth =     {},
OPTnote =         {},
OPTannote =    {}
}

@Article{Esteller00,
author =       {M. Esteller},
title =        {Epigenetic lesions causing genetic lesions in human cancer: promoter hypermethylation of DNA repair genes}, 
journal =   {European Journal of Cancer},
year =         {2000},
OPTkey =       {},
volume =    {36},
number =    {18},
OPTpages =     {},
OPTmonth =     {},
OPTnote =         {},
OPTannote =    {}
}

@Article{Schliepetal03,
author =       {A. Schliep and A. Schonhuth and C. Steinhoff},
title =        {Using hidden markov models to analyze gene expression time course data},
journal =      {Bioinformatics},
year =         {2003},
OPTkey =       {},
OPTvolume =       {},
OPTnumber =    {},
OPTpages =        {},
OPTmonth =     {},
note =      {(submitted)},
OPTannote =    {}
}

@Article{Pinkeletal98,
author =       {D. Pinkel and R. Segraves and D. Sudar, S. Clark and I. Pooleand  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},
title =        {High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarray},
journal =      {Nature Genetics},
year =         {1998},
OPTkey =       {},
volume =       {20},
OPTnumber =    {},
OPTpages =        {},
month =     {Oct},
OPTnote =      {},
OPTannote =    {}
}


@Article{Huetal03,
author =       {J. Hu and V. Khanna and M. W. Jones and U. Surti},
title =        {Comparative study of primary and recurrent ovarian serous carcinomas: comparative genomic hybridization analysis with a potential application for prognosis.},
journal =      {Gynecol Oncol.},
year =         {2003},
OPTkey =       {},
volume =       {89},
number =    {3},
pages =        {369--375},
OPTmonth =     {},
OPTnote =      {},
OPTannote =    {}
}


@Article{Desaietal02,
author =       {K. V. Desai and N. Xiao and W. Wang and L. Gangi and J. Greene and J. I. Powell and R. Dickson and P. Furth and K. Hunter and R. Kucherlapati and R. Simon and E. T. Liu and J. E. Green},
title =        {Initiating oncogenic event determines gene-expression patterns of human breast cancer models},
journal =   {PNAS},
year =         {2002},
OPTkey =       {},
volume =    {10},
number =    {1073},
OPTpages =     {},
OPTmonth =     {},
OPTnote =         {},
OPTannote =    {}
}


@Article{Albertson&Pinkel03,
author =       {D. G. Albertson and D. Pinkel},
title =        {Genomic microarrays in human genetic disease and cancer},
journal =   {Ann Hum Gene},
year =         {2003},
OPTkey =       {},
OPTvolume =    {},
OPTnumber =    {},
OPTpages =     {},
OPTmonth =     {},
note =         {(submitted)},
OPTannote =    {}
}

@Article{Jainetal02,
author =       {A. N. Jain and T. A. Tokuyasu and A. M. Snijders and R. Segraves and D. G. Albertson and D. Pinkel},
title =        {Fully automatic quantification of microarray image data},
journal =   {Genome Research},
year =         {2002},
OPTkey =       {},
volume =    {12},
OPTnumber =    {},
pages =     {325--332},
OPTmonth =     {},
OPTnote =         {},
OPTannote =    {}
}


@Article{Pollack02,
author =       {J. R. Pollack and T. Sorlie and C. M. Perou and C. A. Rees and S. S. Jeffrey and P. E. Lonning and R. Tibshirani and D. Botstein and A-L. Borresen-Dale and P. O. Brown},
title =        {Microarray analysis reveals a major direct role of DNA copy number alteration in the transriptional program of human breast cancers},
journal =   {PNAS},
year =         {2002},
OPTkey =       {},
volume =    {99},
OPTnumber =    {},
pages =     {12963--12968},
OPTmonth =     {},
OPTnote =         {},
OPTannote =    {}
}




@Article{Hodgson01,
author =       {G. Hodgson and J. H. Hager and S. Volik and S. Hariono and M. Wernick and D. Moore and D. G. Albertson and D. Pinkel and C. Collins and D. Hanahan and J. W. Gray},
title =        {Genome scanning with array CGH delineates regional alterations in mouse islet carcinomas},
journal =   {Nature Genetics},
year =         {2001},
OPTkey =       {},
volume =    {929},
OPTnumber =    {},
pages =     {459--464},
OPTmonth =     {},
OPTnote =         {},
OPTannote =    {}
}



@Article{Collinsetal98,
author =       {C. Collins and  J. M. Rommens and  D. Kowbel and  T. Godfrey and  M. Tanner and  S. Hwang and  D. Polikoff and  G. Nonet and  J. Cochran and  K. Myambo and  K. E. Jay and  J. Froula and  T. Cloutier and  W-L. Kuo and  P. Yaswen and  S. Dairkee and  J. Giovanola and  G. B. Hutchinson and  J. Isola and  O-P. Kallioniemi and M. Palazzolo and  C. Martin and  C. Ericsson and  D. Pinkel and  D. Albertson and  W-B. Li and  and J. W. Gray},
title =        {Positional cloning of ZNF217 and NABC1: Genes amplified at
20q13.2 and overexpressed in breast carcinoma},
journal =   {PNAS},
year =    {1998},
OPTkey =       {},
volume =    {95},
OPTnumber =    {},
pages =     {8703--8708},
OPTmonth =     {}, 
OPTnote =         {},
OPTannote =    {}
}


@Article{Nakaoetal04,
author =       {K. Nakao and K. E. Mehta and J. Fridlyand and D. H. Moore and A. N. Jain and A. Lafuente and J. W. Wiencke and J. P. Terdiman and F. M. Waldman},
title =        {High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization},
journal =   {Carcinogenesis},
year =    {2004},
OPTkey =       {},
OPTvolume =    {},
OPTnumber =    {},
OPTpages =     {},
OPTmonth =     {}, 
note =         {Epub in March},
OPTannote =    {}
}




@Article{Fridlyandetal04,
author = {J. Fridlyand and A. M. Snijders and D. Pinkel, D. G. Albertson and
A. N. Jain},
title = {Hidden Markov models approach to the analysis of array CGH
data},
journal = {Journal of Multivariate Analysis},
year = {2004},
OPTkey =       {},
OPTvolume =    {},
OPTnumber =    {},
OPTpages =     {},
OPTmonth =     {},
note =         {in press},
OPTannote =    {}
}
