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%"DNAcopy"
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%Cite:
%"recall that p values
%corresponding to truly null hypotheses should be uniformly
%distributed."
%Cite:
%"'weak dependence' of the p values"
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} 

% set of t-statistics:
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%Cyber t-test:
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title =  {Global variation in copy number in the human genome},
journal =  {Nature},
volume =  {444},
number =  {7118},
pages =  {444-454},
year =  {2006}
}


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title =  {Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome},
journal =  {Am. J. Hum. Genet.},
volume =  {79},
number =  {2},
pages =  {275-290},
year =  {2006}
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@article{Locke:06,
author =  {D. P. Locke and A. J. Sharp and S. A. McCarroll and S. D. McGrath and T. L. Newman and Z. Cheng and S. Schwartz and D. G. Albertson and D. Pinkel and D. M. Altshuler and others},
title =  {Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome},
journal =  {Am. J. Hum. Genet.},
volume =  {79},
number =  {2},
pages =  {275-290},
year =  {2006}
}


@article{Conrad:06,
author =  {D. F. Conrad and T. D. Andrews and N. P. Carter and M. E. Hurles and J. K. Pritchard},
title =  {A high-resolution survey of deletion polymorphism in the human genome},
journal =  {Nature Genet.},
volume =  {38},
number =  {1},
pages =  {75-81},
year =  {2006}
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title =  {Common deletion polymorphisms in the human genome},
journal =  {Nature Genet.},
volume =  {38},
number =  {1},
pages =  {86-92},
year =  {2006}
}

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author =  {S. A. McCarroll and T. N. Hadnott and G. H. Perry and P. C. Sabeti and M. C. Zody and J. C. Barrett and S. Dallaire and S. P. Gabriel and C. Lee and M. J. Daly and others},
title =  {Common deletion polymorphisms in the human genome},
journal =  {Nature Genet.},
volume =  {38},
number =  {1},
pages =  {86-92},
year =  {2006}
}


@article{McCarroll:07,
author =  {S. A. McCarroll and D. M. Altshuler},
title =  {Copy-number variation and association studies of human disease},
journal =  {Nature Genet.},
volume =  {39},
number =  {1},
pages =  {37-42},
year =  {2007}
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author =  {A. J. Sharp and Z. Cheng and E. E. Eichler},
title =  {Structural variation of the human genome},
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pages =  {407-442},
year =  {2006}
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title =  {Nucleosome positioning signals in genomic DNA},
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volume =  {17},
pages =  {1170-1177},
year =  {2007}
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@article{Albert:07,
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journal =  {Nature},
volume =  {446},
number = {7135},
pages =  {572-576},
year =  {2007}
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journal =  {Nature},
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number =  {7104},
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year =  {2006}
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pages =  {78-88},
year =  {2005}
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title =  {Segmental duplications and copy-number variation in the human},
journal =  {The American Journal of Human Genetics},
volume =  {77},
number =  {1},
pages =  {78-88},
year =  {2005}
}


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title =  {Fine-scale structural variation of the human genome},
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title =  {A common inversion under selection in {Europeans}},
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number =  {2},
pages =  {129-137},
year =  {2005}
}


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journal = {Science},
number = {5714},
pages = {1434-1440},
title = {The Influence of {CCL3L1} Gene-Containing Segmental Duplications on {HIV-1/AIDS} Susceptibility},
volume = {307},
year = {2005}
}

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journal = {Science},
number = {5714},
pages = {1434-1440},
title = {The Influence of {CCL3L1} Gene-Containing Segmental Duplications on {HIV-1/AIDS} Susceptibility},
volume = {307},
year = {2005}
}


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author = {T. J. Aitman and R. Dong and T. J. Vyse and P. J. Norsworthy and M. D. Johnson and J. Smith and J. Mangion and C. Roberton-Lowe and A. J. Marshall and E. Petretto and M. D. Hodges and G. Bhangal and S. G. Patel and K. Sheehan-Rooney and M. Duda and P. R. Cook and D. J. Evans and J. Domin and J. Flint and J. J. Boyle and C. D. Pusey and T. H. Cook},
journal = {Nature},
number = {7078},
pages = {851-855},
publisher = {Nature Publishing Group},
title = {Copy number polymorphism in {Fcgr3} predisposes to glomerulonephritis in rats and humans},
volume = {439},
year = {2006}
}


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author = {L. Feuk and A. R. Carson and S. W. Scherer},
journal = {Nature Rev. Genet.},
number = {2},
pages = {85-97},
publisher = {Nature Publishing Group},
title = {Structural variation in the human genome},
volume = {7},
year = {2006}
}


@article{Jacobs:07,
author =  {S. Jacobs and E. R. Thompson and Y. Nannya and G. Yamamoto and R. Pillai and S. Ogawa and D. K. Bailey and I. G. Campbell},
title =  {Genome-Wide, High-Resolution Detection of Copy Number, Loss of Heterozygosity, and Genotypes from Formalin-Fixed, Paraffin-Embedded Tumor Tissue Using Microarrays},
journal =  {Cancer Research},
volume =  {67},
number =  {6},
pages =  {2544-2551},
year =  {2007}
}


@article{Frayling:07,
author =  {T. M. Frayling},
title =  {Genome-wide association studies provide new insights into type 2 diabetes aetiology},
journal =  {Nature Rev. Genet.},
volume =  {8},
number =  {9},
pages =  {657-662},
year =  {2007}
}              
               
             
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title =  {Replication of Genome-Wide Association Signals in {UK} Samples Reveals Risk Loci for Type 2 Diabetes},
journal =  {Science},
volume =  {316},
number =  {5829},
pages =  {1336-1341},
year =  {2007}
}   
       
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title =  {Replication of Genome-Wide Association Signals in {UK} Samples Reveals Risk Loci for Type 2 Diabetes},
journal =  {Science},
volume =  {316},
number =  {5829},
pages =  {1336-1341},
year =  {2007}
}        
              

@article{Scott:07,
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title =  {A Genome-Wide Association Study of Type 2 Diabetes in {Finns} Detects Multiple Susceptibility Variants},
journal =  {Science},
volume =  {316},
number =  {5829},
pages =  {1341-1345},
year =  {2007}
}  

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title =  {A Genome-Wide Association Study of Type 2 Diabetes in {Finns} Detects Multiple Susceptibility Variants},
journal =  {Science},
volume =  {316},
number =  {5829},
pages =  {1341-1345},
year =  {2007}
} 
 


@article{Yang:07,
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title =  {Gene copy-number variation and associated polymorphisms of complement component {C4} in human systemic lupus erythematosus ({SLE}): low copy number is a risk factor for and high copy number is a protective factor against {SLE} susceptibility in {European Americans}},
journal =  {The American Journal of Human Genetics},
volume =  {80},
number =  {6},
pages =  {1037-1054},
year =  {2007}
}  

@article{Yang:07l,
author =  {Y. Yang and E. K. Chung and Y. L. Wu and S. L. Savelli and H. N. Nagaraja and B. Zhou and M. Hebert and K. N. Jones and Y. Shu and K. Kitzmiller and C. A. Blanchong and K. L. McBride and G. C. Higgins and R. M. Rennebohm and R. R. Rice and K. V. Hackshaw and R. A. S. Roubey and J. M. Grossman and B. P. Tsao and D. J. Birmingham and B. H. Rovin and L. A. Hebert and C. Y. Yu},
title =  {Gene copy-number variation and associated polymorphisms of complement component {C4} in human systemic lupus erythematosus ({SLE}): low copy number is a risk factor for and high copy number is a protective factor against {SLE} susceptibility in {European Americans}},
journal =  {The American Journal of Human Genetics},
volume =  {80},
number =  {6},
pages =  {1037-1054},
year =  {2007}
} 


@article{Fanciulli:07,
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title =  {{FCGR3B} copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity},
journal =  {Nature Genet.},
volume =  {39},
number =  {6},
pages =  {721-723},
year =  {2007}
}   

@article{Fanciulli:07l,
author =  {M. Fanciulli and P. J. Norsworthy and E. Petretto and R. Dong and L. Harper and L. Kamesh and J. M. Heward and S. C. Gough and A. de Smith and A. I. Blakemore and P. Froguel and C. J. Owen and S. H. Pearce and L. Teixeira and L. Guillevin and D. S. Graham and C. D. Pusey and H. T. Cook and T. J. Vyse and T. J. Aitman},
title =  {{FCGR3B} copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity},
journal =  {Nature Genet.},
volume =  {39},
number =  {6},
pages =  {721-723},
year =  {2007}
} 


@article{Carvalho:07,
author =  {B. Carvalho and H. Bengtsson and T. P. Speed and R. A. Irizarry},
title =  {Exploration, normalization, and genotype calls of high density oligonucleotide {SNP} array data},
journal =  {Biostatistics},
volume =  {8},
number =  {2},
pages =  {485-499},
year =  {2007}
}   


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volume =  {19},
number =  {18},
pages =  {2397-2403},
year =  {2003}
}   


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title =  {Dynamic model based algorithms for screening and genotyping over 100 k {SNPs} on oligonucleotide microarrays},
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volume =  {21},
number =  {9},
pages =  {1958-1963},
year =  {2005}
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@article{LaFramboise:05,
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title =  {Allele-specific amplification in cancer revealed by {SNP} array analysis},
journal =  {PLoS Computational Biology},
volume =  {1},
number =  {6},
year =  {2005}
}   


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author =  {N. Rabbee and T. P. Speed},
title =  {A genotype calling algorithm for affymetrix {SNP} arrays},
journal =  {Bioinformatics},
volume =  {22},
number =  {1},
pages =  {7-12},
year =  {2006}
}   


@misc{Affymetrix:06,
author =  {Affymetrix},
title =  {{BRLMM}: an improved genotype calling 
method for the genechip human mapping 500k array set},
howpublished = {Affymetrix, Inc., White Paper},
year =  {2006}
}


@article{Nannya:05l,
author =  {Y. Nannya and M. Sanada and K. Nakazaki and N. Hosoya and L. Wang and A. Hangaishi and M. Kurokawa and S. Chiba and D. K. Bailey and G. C. Kennedy and S. Ogawa},
title =  {A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays},
journal =  {Cancer Research},
volume =  {65},
number =  {14},
pages =  {6071-6079},
year =  {2005}
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@article{Nannya:05,
author =  {Y. Nannya and M. Sanada and K. Nakazaki and N. Hosoya and L. Wang and A. Hangaishi and M. Kurokawa and S. Chiba and D. K. Bailey and G. C. Kennedy and  others},
title =  {A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays},
journal =  {Cancer Research},
volume =  {65},
number =  {14},
pages =  {6071-6079},
year =  {2005}
}  


@article{Schuster:07,
author =  {E. F. Schuster and E. Blanc and L. Partridge and J. M. Thornton},
title =  {Estimation and correction of non-specific binding in a large-scale spike-in experiment},
journal =  {Genome Biology},
volume =  {8},
number =  {6},
pages =  {R126.1-R126.19},
year =  {2007}
}   


@article{Hochreiter:06,
author =  {S. Hochreiter and D.-A. Clevert and K. Obermayer},
title =  {A new summarization method for {Affymetrix} probe level data},
journal =  {Bioinformatics},
volume =  {22},
number =  {8},
pages =  {943-949},
year =  {2006}
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@article{Hochreiter:07,
author =  {S. Hochreiter and M. Heusel and K. Obermayer},
title =  {Fast model-based protein homology detection without alignment},
journal =  {Bioinformatics},
volume =  {23},
number =  {14},
pages =  {1728-1736},
year =  {2007}
}   

@article{Talloen:07,
author =  {W. Talloen and D.-A. Clevert and S. Hochreiter and D. Amaratunga and L. Bijnens and S. Kass and H. W. H. G{\"o}hlmann},
title =  {{I/NI}-calls for the exclusion of non-informative genes: a highly effective feature filtering tool for microarray data},
journal =  {Bioinformatics},
volume = {23},
number = {21},
pages = {2897-2902},
year =  {2007}
}   

@misc{Clevert:07,
author =  {D.-A. Clevert and S. Hochreiter},
title =  {{FARMS}: a probabilistic latent variable model for summarizing {Affymetrix} array data at probe level},
howpublished = {15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)},
year =  {2007}
}


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author =  {J. A. Bailey and Z. Gu and R. A. Clark and K. Reinert and R. V. Samonte and S. Schwartz and M. D. Adams and E. W. Myers and P. W. Li and E. E. Eichler},
title =  {Recent Segmental Duplications in the Human Genome},
journal =  {Science},
volume =  {297},
number =  {5583},
pages =  {1003-1007},
year =  {2002}
}   


@article{Check:05,
author =  {E. Check},
title =  {News Feature: Patchwork people},
journal =  {Nature},
volume =  {437},
number =  {7062},
pages =  {1084-1086},
year =  {2005}
}   


@article{Zhao:04,
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title =  {An Integrated View of Copy Number and Allelic Alterations in the Cancer Genome Using Single Nucleotide Polymorphism Arrays},
journal =  {Cancer Research},
volume =  {64},
number =  {9},
pages =  {3060-3071},
year =  {2004}
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@article{Mullighan:07,
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title =  {Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia},
journal =  {Nature},
volume =  {446},
number =  {7137},
pages =  {758-764},
year =  {2007}
}


@article{Yamamoto:07,
author =  {Go Yamamoto, Yasuhito Nannya, Motohiro Kato, Masashi Sanada, Ross L. Levine, Norihiko Kawamata, Akira Hangaishi, Mineo Kurokawa, Shigeru Chiba, D. Gary Gilliland, H. Phillip Koeffler, and Seishi Ogawa},
title =  {Highly sensitive method for genome-wide detection of allelic composition in non-paired, primary tumor specimens using {Affymetrix (R) SNP} genotyping microarrays},
journal =  {American Journal of Human Genetics},
volume =  {81},
number =  {1},
pages =  {114-126},
year =  {2007}
}


@inproceedings{Hochreiter:01icann1,
author =  {S. Hochreiter and M. C. Mozer},
title =  {A discrete probabilistic memory model for
discovering dependencies in time},
booktitle =  {International Conference on Artificial Neural Networks},
editor={G. Dorffner and H. Bischof and K. Hornik},
publisher={Springer},
pages = {661-668},
year = {2001}}



@article{Leslie:02,
author = {C. Leslie and E. Eskin and W. S. Noble},
title = {The spectrum kernel: {A} string kernel for {SVM} protein
classification},
journal = {Proceedings of the Pacific Symposium on Biocomputing},
year = {2002}
}


@article{Leslie:04b,
author =  {C. Leslie and E. Eskin and A. Cohen and J. Weston and W. S. Noble},
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journal =  {Bioinformatics},
year =  {2004},
volume =  {20},
number =  {4},
pages =  {467-476}}


@article{Ratsch:07,
author =  {G. R{\"a}tsch and S. Sonnenburg and J. Srinivasan and H. Witte and K.-R. M{\"u}ller and R. Sommer and B. Sch{\"o}lkopf},
title =  {Improving the {C. elegans} genome annotation using machine learning},
journal =  {PLoS Computational Biology},
volume =  {3},
number =  {3},
pages =  {e20},
year =  {2007}
}


@article{Ratsch:05,
author =  {G. R{\"a}tsch and S. Sonnenburg and B. Sch{\"o}lkopf},
title =  {{RASE}: Recognition of alternatively Spliced Exons in {C. elegans}},
journal =  {Bioinformatics},
volume =  {21},
number =  {Suppl 1},
pages =  {i369-i377},
year =  {2005}
}

@article{Hochreiter:06b,
author =  {S. Hochreiter and K. Obermayer},
title =  {Support Vector Machines for Dyadic Data},
journal = {Neural Comput
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volume = {18},
number = {6},
pages = {1472-1510},
year = {2006}
}


@incollection{Hochreiter:03d,
author = {S. Hochreiter and K. Obermayer},
title = {Feature Selection and Classification on Matrix Data:
{F}rom Large Margins to Small Covering Numbers},
booktitle = {Advances in Neural Information Processing Systems 15},
editor = {S. Becker and S. Thrun and K. Obermayer},
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