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CNVeM: copy number variation detection using uncertainty of read mapping.

Wang Z, Hormozdiari F, Yang WY, Halperin E, Eskin E.

J Comput Biol. 2013 Mar;20(3):224-36. doi: 10.1089/cmb.2012.0258. Epub 2013 Feb 19.


Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions.

He D, Hormozdiari F, Furlotte N, Eskin E.

Bioinformatics. 2011 Jun 1;27(11):1513-20. doi: 10.1093/bioinformatics/btr169. Epub 2011 Apr 19.


Shape-based retrieval of CNV regions in read coverage data.

Hong S, Yoon J, Hong D, Lee U, Kim B, Park S.

Int J Data Min Bioinform. 2014;9(3):254-76.


Detecting copy number variation with mated short reads.

Medvedev P, Fiume M, Dzamba M, Smith T, Brudno M.

Genome Res. 2010 Nov;20(11):1613-22. doi: 10.1101/gr.106344.110. Epub 2010 Aug 30.


CNV-CH: A Convex Hull Based Segmentation Approach to Detect Copy Number Variations (CNV) Using Next-Generation Sequencing Data.

Sinha R, Samaddar S, De RK.

PLoS One. 2015 Aug 20;10(8):e0135895. doi: 10.1371/journal.pone.0135895. eCollection 2015.


AREM: aligning short reads from ChIP-sequencing by expectation maximization.

Newkirk D, Biesinger J, Chon A, Yokomori K, Xie X.

J Comput Biol. 2011 Nov;18(11):1495-505. doi: 10.1089/cmb.2011.0185. Epub 2011 Oct 28.


CNV-guided multi-read allocation for ChIP-seq.

Zhang Q, KeleĊŸ S.

Bioinformatics. 2014 Oct 15;30(20):2860-7. doi: 10.1093/bioinformatics/btu402. Epub 2014 Jun 24.


CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.

Abyzov A, Urban AE, Snyder M, Gerstein M.

Genome Res. 2011 Jun;21(6):974-84. doi: 10.1101/gr.114876.110. Epub 2011 Feb 7.


Copy number variation detection using next generation sequencing read counts.

Wang H, Nettleton D, Ying K.

BMC Bioinformatics. 2014 Apr 14;15:109. doi: 10.1186/1471-2105-15-109.


Quantifying copy number variations using a hidden Markov model with inhomogeneous emission distributions.

McCallum KJ, Wang JP.

Biostatistics. 2013 Jul;14(3):600-11. doi: 10.1093/biostatistics/kxt003. Epub 2013 Feb 20.


CNV-TV: a robust method to discover copy number variation from short sequencing reads.

Duan J, Zhang JG, Deng HW, Wang YP.

BMC Bioinformatics. 2013 May 2;14:150. doi: 10.1186/1471-2105-14-150.


Modeling the next generation sequencing read count data for DNA copy number variant study.

Ji T, Chen J.

Stat Appl Genet Mol Biol. 2015 Aug;14(4):361-74. doi: 10.1515/sagmb-2014-0054.


An initial comparative map of copy number variations in the goat (Capra hircus) genome.

Fontanesi L, Martelli PL, Beretti F, Riggio V, Dall'Olio S, Colombo M, Casadio R, Russo V, Portolano B.

BMC Genomics. 2010 Nov 17;11:639. doi: 10.1186/1471-2164-11-639.


De novo detection of copy number variation by co-assembly.

Nijkamp JF, van den Broek MA, Geertman JM, Reinders MJ, Daran JM, de Ridder D.

Bioinformatics. 2012 Dec 15;28(24):3195-202. doi: 10.1093/bioinformatics/bts601. Epub 2012 Oct 9.


Copy number variation of individual cattle genomes using next-generation sequencing.

Bickhart DM, Hou Y, Schroeder SG, Alkan C, Cardone MF, Matukumalli LK, Song J, Schnabel RD, Ventura M, Taylor JF, Garcia JF, Van Tassell CP, Sonstegard TS, Eichler EE, Liu GE.

Genome Res. 2012 Apr;22(4):778-90. doi: 10.1101/gr.133967.111. Epub 2012 Feb 2.


Genome-wide algorithm for detecting CNV associations with diseases.

Xu Y, Peng B, Fu Y, Amos CI.

BMC Bioinformatics. 2011 Aug 9;12:331. doi: 10.1186/1471-2105-12-331.


Read count approach for DNA copy number variants detection.

Magi A, Tattini L, Pippucci T, Torricelli F, Benelli M.

Bioinformatics. 2012 Feb 15;28(4):470-8. doi: 10.1093/bioinformatics/btr707. Epub 2011 Dec 23.


Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data.

Caboche S, Audebert C, Lemoine Y, Hot D.

BMC Genomics. 2014 Apr 5;15:264. doi: 10.1186/1471-2164-15-264.


Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm.

Magi A, Benelli M, Yoon S, Roviello F, Torricelli F.

Nucleic Acids Res. 2011 May;39(10):e65. doi: 10.1093/nar/gkr068. Epub 2011 Feb 14.


A comprehensive survey of copy number variation in 18 diverse pig populations and identification of candidate copy number variable genes associated with complex traits.

Chen C, Qiao R, Wei R, Guo Y, Ai H, Ma J, Ren J, Huang L.

BMC Genomics. 2012 Dec 27;13:733. doi: 10.1186/1471-2164-13-733.

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