@ARTICLE{Zhou2018-hd,
  title     = "Whole-genome sequencing analysis of {CNV} using low-coverage and
               paired-end strategies is efficient and outperforms array-based
               {CNV} analysis",
  author    = "Zhou, Bo and Ho, Steve S and Zhang, Xianglong and Pattni, Reenal
               and Haraksingh, Rajini R and Urban, Alexander E",
  journal   = "J. Med. Genet.",
  publisher = "BMJ Publishing Group Ltd",
  volume    =  55,
  number    =  11,
  pages     = "735--743",
  month     =  nov,
  year      =  2018,
  keywords  = "array Cgh (acgh); copy-number variation (cnv); discordant
               read-pair analysis; mate-pair sequencing; read-depth analysis",
  language  = "en",
  doi       = "10.1136/jmedgenet-2018-105272"
}

@ARTICLE{da-Silva2018-bb,
  title     = "{CNVs} are associated with genomic architecture in a songbird",
  author    = "da Silva, Vinicius H and Laine, Veronika N and Bosse, Mirte and
               van Oers, Kees and Dibbits, Bert and Visser, Marcel E and M A
               Crooijmans, Richard P and Groenen, Martien A M",
  journal   = "BMC Genomics",
  publisher = "BioMed Central",
  volume    =  19,
  number    =  1,
  pages     =  195,
  month     =  mar,
  year      =  2018,
  keywords  = "Duplication; Genetic variation; Inheritance; Parus major;
               Recombination",
  language  = "en",
  doi       = "10.1186/s12864-018-4577-1"
}

@ARTICLE{Geistlinger2018-vg,
  title     = "Widespread modulation of gene expression by copy number variation
               in skeletal muscle",
  author    = "Geistlinger, Ludwig and da Silva, Vinicius Henrique and Cesar,
               Aline Silva Mello and Tizioto, Polyana Cristine and Waldron, Levi
               and Zimmer, Ralf and Regitano, Luciana Correia de Almeida and
               Coutinho, Luiz Lehmann",
  journal   = "Sci. Rep.",
  publisher = "Nature Publishing Group",
  volume    =  8,
  number    =  1,
  pages     =  1399,
  month     =  jan,
  year      =  2018,
  language  = "en",
  doi       = "10.1038/s41598-018-19782-4"
}

@ARTICLE{Zhang2019-no,
  title     = "{EnsembleCNV}: an ensemble machine learning algorithm to identify
               and genotype copy number variation using {SNP} array data",
  author    = "Zhang, Zhongyang and Cheng, Haoxiang and Hong, Xiumei and Di
               Narzo, Antonio F and Franzen, Oscar and Peng, Shouneng and
               Ruusalepp, Arno and Kovacic, Jason C and Bjorkegren, Johan L M
               and Wang, Xiaobin and Hao, Ke",
  journal   = "Nucleic Acids Res.",
  publisher = "Oxford University Press (OUP)",
  volume    =  47,
  number    =  7,
  pages     = "e39",
  month     =  apr,
  year      =  2019,
  keywords  = "genome; genotype; single nucleotide polymorphism; genotype
               determination; copy number polymorphism; datasets; genome-wide
               association study; quality control; machine learning",
  language  = "en",
  doi       = "10.1093/nar/gkz068"
}

@ARTICLE{Wang2007-ik,
  title     = "{PennCNV}: an integrated hidden Markov model designed for
               high-resolution copy number variation detection in whole-genome
               {SNP} genotyping data",
  author    = "Wang, Kai and Li, Mingyao and Hadley, Dexter and Liu, Rui and
               Glessner, Joseph and Grant, Struan F A and Hakonarson, Hakon and
               Bucan, Maja",
  journal   = "Genome Res.",
  publisher = "Cold Spring Harbor Laboratory",
  volume    =  17,
  number    =  11,
  pages     = "1665--1674",
  month     =  nov,
  year      =  2007,
  language  = "en",
  doi       = "10.1101/gr.6861907"
}

@ARTICLE{Becker2018-dh,
  title     = "{FusorSV}: an algorithm for optimally combining data from
               multiple structural variation detection methods",
  author    = "Becker, Timothy and Lee, Wan-Ping and Leone, Joseph and Zhu,
               Qihui and Zhang, Chengsheng and Liu, Silvia and Sargent, Jack and
               Shanker, Kritika and Mil-Homens, Adam and Cerveira, Eliza and
               Ryan, Mallory and Cha, Jane and Navarro, Fabio C P and Galeev,
               Timur and Gerstein, Mark and Mills, Ryan E and Shin, Dong-Guk and
               Lee, Charles and Malhotra, Ankit",
  journal   = "Genome Biol.",
  publisher = "BioMed Central",
  volume    =  19,
  number    =  1,
  pages     =  38,
  month     =  mar,
  year      =  2018,
  keywords  = "Copy number variation; Genome rearrangements; Next generation
               sequencing; Structural variation",
  language  = "en",
  doi       = "10.1186/s13059-018-1404-6"
}

@ARTICLE{Layer2014-yy,
  title     = "{LUMPY}: a probabilistic framework for structural variant
               discovery",
  author    = "Layer, Ryan M and Chiang, Colby and Quinlan, Aaron R and Hall,
               Ira M",
  journal   = "Genome Biol.",
  publisher = "Springer Nature",
  volume    =  15,
  number    =  6,
  pages     = "R84",
  month     =  jun,
  year      =  2014,
  language  = "en",
  doi       = "10.1186/gb-2014-15-6-r84"
}

@ARTICLE{Trost2018-zk,
  title     = "A comprehensive workflow for read depth-based identification of
               copy-number variation from whole-genome sequence data",
  author    = "Trost, Brett and Walker, Susan and Wang, Zhuozhi and
               Thiruvahindrapuram, Bhooma and MacDonald, Jeffrey R and Sung,
               Wilson W L and Pereira, Sergio L and Whitney, Joe and Chan, Ada J
               S and Pellecchia, Giovanna and Reuter, Miriam S and Lok, Si and
               Yuen, Ryan K C and Marshall, Christian R and Merico, Daniele and
               Scherer, Stephen W",
  journal   = "Am. J. Hum. Genet.",
  publisher = "Elsevier",
  volume    =  102,
  number    =  1,
  pages     = "142--155",
  month     =  jan,
  year      =  2018,
  keywords  = "CNV; SV; WGS; copy-number variation; read depth; structural
               variation; variation detection; whole-genome sequencing",
  language  = "en",
  doi       = "10.1016/j.ajhg.2017.12.007"
}

@ARTICLE{Silva2016-rc,
  title     = "Genome-wide detection of {CNVs} and their association with meat
               tenderness in Nelore cattle",
  author    = "Silva, Vinicius Henrique da and Regitano, Luciana Correia de
               Almeida and Geistlinger, Ludwig and P\'{e}rtille, F\'{a}bio and
               Giachetto, Poliana Fernanda and Brassaloti, Ricardo Augusto and
               Morosini, Nat\'{a}lia Silva and Zimmer, Ralf and Coutinho, Luiz
               Lehmann",
  journal   = "PLoS One",
  publisher = "Public Library of Science (PLoS)",
  volume    =  11,
  number    =  6,
  pages     = "e0157711",
  month     =  jun,
  year      =  2016,
  language  = "en",
  doi       = "10.1371/journal.pone.0157711"
}

@ARTICLE{Abyzov2011-xs,
  title     = "{CNVnator}: an approach to discover, genotype, and characterize
               typical and atypical {CNVs} from family and population genome
               sequencing",
  author    = "Abyzov, Alexej and Urban, Alexander E and Snyder, Michael and
               Gerstein, Mark",
  journal   = "Genome Res.",
  publisher = "Cold Spring Harbor Laboratory",
  volume    =  21,
  number    =  6,
  pages     = "974--984",
  month     =  jun,
  year      =  2011,
  language  = "en",
  doi       = "10.1101/gr.6861907"
}

@ARTICLE{Nica2013-dn,
  title     = "Expression quantitative trait loci: present and future",
  author    = "Nica, Alexandra C and Dermitzakis, Emmanouil T",
  journal   = "Philos. Trans. R. Soc. Lond. B Biol. Sci.",
  publisher = "The Royal Society",
  volume    =  368,
  number    =  1620,
  pages     =  20120362,
  month     =  may,
  year      =  2013,
  keywords  = "expression quantitative trait loci; genetics; regulation",
  language  = "en",
  doi       = "10.1098/rstb.2012.0362"
}

@ARTICLE{Sudmant2015-pf,
  title     = "An integrated map of structural variation in 2,504 human genomes",
  author    = "Sudmant, Peter H and Rausch, Tobias and Gardner, Eugene J and
               Handsaker, Robert E and Abyzov, Alexej and Huddleston, John and
               Zhang, Yan and Ye, Kai and Jun, Goo and Fritz, Markus Hsi-Yang
               and Konkel, Miriam K and Malhotra, Ankit and St{\"{u}}tz, Adrian
               M and Shi, Xinghua and Casale, Francesco Paolo and Chen, Jieming
               and Hormozdiari, Fereydoun and Dayama, Gargi and Chen, Ken and
               Malig, Maika and Chaisson, Mark J P and Walter, Klaudia and
               Meiers, Sascha and Kashin, Seva and Garrison, Erik and Auton,
               Adam and Lam, Hugo Y K and Mu, Xinmeng Jasmine and Alkan, Can and
               Antaki, Danny and Bae, Taejeong and Cerveira, Eliza and Chines,
               Peter and Chong, Zechen and Clarke, Laura and Dal, Elif and Ding,
               Li and Emery, Sarah and Fan, Xian and Gujral, Madhusudan and
               Kahveci, Fatma and Kidd, Jeffrey M and Kong, Yu and Lameijer,
               Eric-Wubbo and McCarthy, Shane and Flicek, Paul and Gibbs,
               Richard A and Marth, Gabor and Mason, Christopher E and Menelaou,
               Androniki and Muzny, Donna M and Nelson, Bradley J and Noor,
               Amina and Parrish, Nicholas F and Pendleton, Matthew and
               Quitadamo, Andrew and Raeder, Benjamin and Schadt, Eric E and
               Romanovitch, Mallory and Schlattl, Andreas and Sebra, Robert and
               Shabalin, Andrey A and Untergasser, Andreas and Walker, Jerilyn A
               and Wang, Min and Yu, Fuli and Zhang, Chengsheng and Zhang, Jing
               and Zheng-Bradley, Xiangqun and Zhou, Wanding and Zichner, Thomas
               and Sebat, Jonathan and Batzer, Mark A and McCarroll, Steven A
               and {1000 Genomes Project Consortium} and Mills, Ryan E and
               Gerstein, Mark B and Bashir, Ali and Stegle, Oliver and Devine,
               Scott E and Lee, Charles and Eichler, Evan E and Korbel, Jan O",
  journal   = "Nature",
  publisher = "Nature Publishing Group",
  volume    =  526,
  number    =  7571,
  pages     = "75--81",
  month     =  oct,
  year      =  2015,
  language  = "en",
  doi       = "10.1038/nature15394"
}

@ARTICLE{Carter2012-hm,
  title     = "Absolute quantification of somatic {DNA} alterations in human
               cancer",
  author    = "Carter, Scott L and Cibulskis, Kristian and Helman, Elena and
               McKenna, Aaron and Shen, Hui and Zack, Travis and Laird, Peter W
               and Onofrio, Robert C and Winckler, Wendy and Weir, Barbara A and
               Beroukhim, Rameen and Pellman, David and Levine, Douglas A and
               Lander, Eric S and Meyerson, Matthew and Getz, Gad",
  journal   = "Nat. Biotechnol.",
  publisher = "Springer Science and Business Media LLC",
  volume    =  30,
  number    =  5,
  pages     = "413--421",
  month     =  may,
  year      =  2012,
  language  = "en",
  doi       = "10.1038/nbt.2203"
}


@ARTICLE{Kim2012-kx,
  title     = "{CNVRuler}: a copy number variation-based case-control
               association analysis tool",
  author    = "Kim, Ji-Hong and Hu, Hae-Jin and Yim, Seon-Hee and Bae, Joon Seol
               and Kim, Seon-Young and Chung, Yeun-Jun",
  journal   = "Bioinformatics",
  publisher = "Oxford University Press (OUP)",
  volume    =  28,
  number    =  13,
  pages     = "1790--1792",
  month     =  jul,
  year      =  2012,
  language  = "en",
  doi       = "10.1093/bioinformatics/bts239"
}

@ARTICLE{Conrad2010-lz,
  title     = "Origins and functional impact of copy number variation in the
               human genome",
  author    = "Conrad, Donald F and Pinto, Dalila and Redon, Richard and Feuk,
               Lars and Gokcumen, Omer and Zhang, Yujun and Aerts, Jan and
               Andrews, T Daniel and Barnes, Chris and Campbell, Peter and
               Fitzgerald, Tomas and Hu, Min and Ihm, Chun Hwa and Kristiansson,
               Kati and Macarthur, Daniel G and Macdonald, Jeffrey R and Onyiah,
               Ifejinelo and Pang, Andy Wing Chun and Robson, Sam and Stirrups,
               Kathy and Valsesia, Armand and Walter, Klaudia and Wei, John and
               {Wellcome Trust Case Control Consortium} and Tyler-Smith, Chris
               and Carter, Nigel P and Lee, Charles and Scherer, Stephen W and
               Hurles, Matthew E",
  journal   = "Nature",
  publisher = "Nature Publishing Group",
  volume    =  464,
  number    =  7289,
  pages     = "704--712",
  month     =  apr,
  year      =  2010,
  language  = "en",
  doi       = "10.1038/nature08516"
}

@ARTICLE{Cahan2009-ke,
  title     = "The impact of copy number variation on local gene expression in
               mouse hematopoietic stem and progenitor cells",
  author    = "Cahan, Patrick and Li, Yedda and Izumi, Masayo and Graubert,
               Timothy A",
  journal   = "Nat. Genet.",
  publisher = "Springer Science and Business Media LLC",
  volume    =  41,
  number    =  4,
  pages     = "430--437",
  month     =  apr,
  year      =  2009,
  language  = "en",
  doi       = "10.1038/ng.350"
}

@ARTICLE{Beroukhim2007-ea,
  title     = "Assessing the significance of chromosomal aberrations in cancer:
               methodology and application to glioma",
  author    = "Beroukhim, Rameen and Getz, Gad and Nghiemphu, Leia and
               Barretina, Jordi and Hsueh, Teli and Linhart, David and Vivanco,
               Igor and Lee, Jeffrey C and Huang, Julie H and Alexander, Sethu
               and Du, Jinyan and Kau, Tweeny and Thomas, Roman K and Shah,
               Kinjal and Soto, Horacio and Perner, Sven and Prensner, John and
               Debiasi, Ralph M and Demichelis, Francesca and Hatton, Charlie
               and Rubin, Mark A and Garraway, Levi A and Nelson, Stan F and
               Liau, Linda and Mischel, Paul S and Cloughesy, Tim F and
               Meyerson, Matthew and Golub, Todd A and Lander, Eric S and
               Mellinghoff, Ingo K and Sellers, William R",
  journal   = "Proc. Natl. Acad. Sci. U. S. A.",
  publisher = "Proceedings of the National Academy of Sciences",
  volume    =  104,
  number    =  50,
  pages     = "20007--20012",
  month     =  dec,
  year      =  2007,
  language  = "en",
  doi       = "10.1073/pnas.0710052104"
}
