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Volumn 40, Issue 9, 2012, Pages

Cn.MOPS: Mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; GUANINE;

EID: 84861400043     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks003     Document Type: Article
Times cited : (345)

References (33)
  • 2
    • 79951481957 scopus 로고    scopus 로고
    • Initial impact of the sequencing of the human genome
    • Lander, E.S. (2011) Initial impact of the sequencing of the human genome. Nature, 470, 187-197.
    • (2011) Nature , vol.470 , pp. 187-197
    • Lander, E.S.1
  • 4
    • 77949481052 scopus 로고    scopus 로고
    • Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
    • Bullard, J.H., Purdom, E., Hansen, K.D. and Dudoit, S. (2010) Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics, 11, 94.
    • (2010) BMC Bioinformatics , vol.11 , pp. 94
    • Bullard, J.H.1    Purdom, E.2    Hansen, K.D.3    Dudoit, S.4
  • 5
    • 79959473093 scopus 로고    scopus 로고
    • Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling
    • Labaj, P.P., Leparc, G.G., Linggi, B.E., Markillie, L.M., Wiley, S.H. and Kreil, D.P. (2011) Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling. Bioinformatics, 27, i383-i391.
    • (2011) Bioinformatics , vol.27
    • Labaj, P.P.1    Leparc, G.G.2    Linggi, B.E.3    Markillie, L.M.4    Wiley, S.H.5    Kreil, D.P.6
  • 14
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    • Dohm, J.C., Lottaz, C., Borodina, T. and Himmelbauer, H. (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res., 36, e105.
    • (2008) Nucleic Acids Res. , vol.36
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4
  • 15
    • 69749122557 scopus 로고    scopus 로고
    • Sensitive and accurate detection of copy number variants using read depth of coverage
    • Yoon, S., Xuan, Z., Makarov, V., Ye, K. and Sebat, J. (2009) Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res., 19, 1586-1592.
    • (2009) Genome Res. , vol.19 , pp. 1586-1592
    • Yoon, S.1    Xuan, Z.2    Makarov, V.3    Ye, K.4    Sebat, J.5
  • 16
    • 79961202047 scopus 로고    scopus 로고
    • Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm
    • Magi, A., Benelli, M., Yoon, S., Roviello, F. and Torricelli, F. (2011) Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm. Nucleic Acids Res., 39, e65.
    • (2011) Nucleic Acids Res. , vol.39
    • Magi, A.1    Benelli, M.2    Yoon, S.3    Roviello, F.4    Torricelli, F.5
  • 17
    • 77956331627 scopus 로고    scopus 로고
    • Integrating common and rare genetic variation in diverse human populations
    • The International HapMap 3 Consortium
    • The International HapMap 3 Consortium (2010) Integrating common and rare genetic variation in diverse human populations. Nature, 467, 52-58.
    • (2010) Nature , vol.467 , pp. 52-58
  • 18
    • 77955635446 scopus 로고    scopus 로고
    • RSW-seq: Algorithm for detection of copy number alterations in deep sequencing data
    • Kim, T.-M., Luquette, L.J., Xi, R. and Park, P.J. (2010) rSW-seq: algorithm for detection of copy number alterations in deep sequencing data. BMC Bioinformatics, 11, 432.
    • (2010) BMC Bioinformatics , vol.11 , pp. 432
    • Kim, T.-M.1    Luquette, L.J.2    Xi, R.3    Park, P.J.4
  • 19
    • 79951748341 scopus 로고    scopus 로고
    • CNAseg- A novel framework for identification of copy number changes in cancer from second-generation sequencing data
    • Ivakhno, S., Royce, T., Cox, A.J., Evers, D.J., Cheetham, R.K. and Tavar, S. (2010) CNAseg- A novel framework for identification of copy number changes in cancer from second-generation sequencing data. Bioinformatics, 26, 3051-3058.
    • (2010) Bioinformatics , vol.26 , pp. 3051-3058
    • Ivakhno, S.1    Royce, T.2    Cox, A.J.3    Evers, D.J.4    Cheetham, R.K.5    Tavar, S.6
  • 20
    • 64849083125 scopus 로고    scopus 로고
    • CNV-Seq, a new method to detect copy number variation using high-throughput sequencing
    • Xie, C. and Tammi, M.T. (2009) CNV-Seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics, 10, 80.
    • (2009) BMC Bioinformatics , vol.10 , pp. 80
    • Xie, C.1    Tammi, M.T.2
  • 22
    • 85162013348 scopus 로고    scopus 로고
    • Catching change-points with lasso
    • Platt, J.C., Koller, D., Singer, Y. and Roweis, S. (eds) MIT Press, Cambridge, MA
    • Harchaoui, Z. and Levy-Leduc, C. (2008) Catching Change-points with Lasso. In: Platt, J.C., Koller, D., Singer, Y. and Roweis, S. (eds), Advances in Neural Information Processing Systems, Vol. 20. MIT Press, Cambridge, MA, pp. 617-624.
    • (2008) Advances in Neural Information Processing Systems , vol.20 , pp. 617-624
    • Harchaoui, Z.1    Levy-Leduc, C.2
  • 23
    • 78649309503 scopus 로고    scopus 로고
    • Detecting copy number variation with mated short reads
    • Medvedev, P., Fiume, M., Dzamba, M., Smith, T. and Brudno, M. (2010) Detecting copy number variation with mated short reads. Genome Res., 20, 1613-1622.
    • (2010) Genome Res. , vol.20 , pp. 1613-1622
    • Medvedev, P.1    Fiume, M.2    Dzamba, M.3    Smith, T.4    Brudno, M.5
  • 25
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M. and Salzberg, S. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
    • (2009) Genome Biol. , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.4
  • 26
    • 84975742565 scopus 로고    scopus 로고
    • A map of human genome variation from population-scale sequencing
    • The 1000 Genomes Project Consortium
    • The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073.
    • (2010) Nature , vol.467 , pp. 1061-1073
  • 27
    • 4344610653 scopus 로고    scopus 로고
    • A new test for the Poisson distribution
    • Brown, L. and Zhao, L. (2002) A new test for the Poisson distribution. Sankhya Ser. A, 64, 611-625.
    • (2002) Sankhya Ser. A , vol.64 , pp. 611-625
    • Brown, L.1    Zhao, L.2
  • 29
    • 33645823677 scopus 로고    scopus 로고
    • A new summarization method for Affymetrix probe level data
    • Hochreiter, S., Clevert, D.-A. and Obermayer, K. (2006) A new summarization method for Affymetrix probe level data. Bioinformatics, 22, 943-949.
    • (2006) Bioinformatics , vol.22 , pp. 943-949
    • Hochreiter, S.1    Clevert, D.-A.2    Obermayer, K.3
  • 30
    • 36448929060 scopus 로고    scopus 로고
    • I/NI-calls for the exclusion of non-informative genes: A highly effective filtering tool for microarray data
    • DOI 10.1093/bioinformatics/btm478
    • Talloen, W., Clevert, D.-A., Hochreiter, S., Amaratunga, D., Bijnens, L., Kass, S. and Göhlmann, H. (2007) I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data. Bioinformatics, 23, 2897-2902. (Pubitemid 350162896)
    • (2007) Bioinformatics , vol.23 , Issue.21 , pp. 2897-2902
    • Talloen, W.1    Clevert, D.-A.2    Hochreiter, S.3    Amaratunga, D.4    Bijnens, L.5    Kass, S.6    Gohlmann, H.W.H.7
  • 32
    • 34147104969 scopus 로고    scopus 로고
    • A faster circular binary segmentation algorithm for the analysis of array CGH data
    • DOI 10.1093/bioinformatics/btl646
    • Venkatraman, E.S. and Olshen, A.B. (2007) A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics, 23, 657-663. (Pubitemid 46554715)
    • (2007) Bioinformatics , vol.23 , Issue.6 , pp. 657-663
    • Venkatraman, E.S.1    Olshen, A.B.2
  • 33
    • 79957950801 scopus 로고    scopus 로고
    • SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples
    • Le, S.Q. and Durbin, R. (2011) SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples. Genome Res., 21, 952-960.
    • (2011) Genome Res. , vol.21 , pp. 952-960
    • Le, S.Q.1    Durbin, R.2


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