Inferring Somatic Signatures from Single Nucleotide Variant Calls (original) (raw)

References

[1] L. Alexandrov. WTSI Mutational Signature Framework, Oct. 2012. [ http ]
[2] L. B. Alexandrov, S. Nik-Zainal, D. C. Wedge, S. A. J. R. Aparicio, S. Behjati, A. V. Biankin, G. R. Bignell, N. Bolli, A. Borg, A.-L. Børresen-Dale, S. Boyault, B. Burkhardt, A. P. Butler, C. Caldas, H. R. Davies, C. Desmedt, R. Eils, J. E. Eyfjörd, J. A. Foekens, M. Greaves, F. Hosoda, B. Hutter, T. Ilicic, S. Imbeaud, M. Imielinsk, N. Jäger, D. T. W. Jones, D. Jones, S. Knappskog, M. Kool, S. R. Lakhani, C. López-Otín, S. Martin, N. C. Munshi, H. Nakamura, P. A. Northcott, M. Pajic, E. Papaemmanuil, A. Paradiso, J. V. Pearson, X. S. Puente, K. Raine, M. Ramakrishna, A. L. Richardson, J. Richter, P. Rosenstiel, M. Schlesner, T. N. Schumacher, P. N. Span, J. W. Teague, Y. Totoki, A. N. J. Tutt, R. Valdés-Mas, M. M. van Buuren, L. v. . Veer, A. Vincent-Salomon, N. Waddell, L. R. Yates, Australian Pancreatic Cancer Genome Initiative, ICGC Breast Cancer Consortium, ICGC MMML-Seq Consortium, Icgc PedBrain, J. Zucman-Rossi, P. Andrew Futreal, U. McDermott, P. Lichter, M. Meyerson, S. M. Grimmond, R. Siebert, E. Campo, T. Shibata, S. M. Pfister, P. J. Campbell, and M. R. Stratton. Signatures of mutational processes in human cancer.Nature, 500(7463):415-421, Aug. 2013. [ DOI | .html ]
[3] L. B. Alexandrov, S. Nik-Zainal, D. C. Wedge, P. J. Campbell, and M. R. Stratton. Deciphering Signatures of Mutational Processes Operative in Human Cancer.Cell Reports, 3(1):246-259, Jan. 2013. [ DOI | http ]
[4] K. Cibulskis, M. S. Lawrence, S. L. Carter, A. Sivachenko, D. Jaffe, C. Sougnez, S. Gabriel, M. Meyerson, E. S. Lander, and G. Getz. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples.Nature Biotechnology, advance online publication, Feb. 2013. [ DOI | .html ]
[5] A. Fischer, C. J. Illingworth, P. J. Campbell, and V. Mustonen. EMu: probabilistic inference of mutational processes and their localization in the cancer genome.Genome biology, 14(4):R39, Apr. 2013. [ DOI ]
[6] A. Fischer. EMu: Expectation-Maximisation inference of mutational signatures, 2013. [ http ]
[7] R. Gaujoux and C. Seoighe. A flexible R package for nonnegative matrix factorization.BMC Bioinformatics, 11(1):367, July 2010. [ DOI | http ]
[8] R. C. Gentleman, V. J. Carey, D. M. Bates, B. Bolstad, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, J. Gentry, K. Hornik, T. Hothorn, W. Huber, S. Iacus, R. Irizarry, F. Leisch, C. Li, M. Maechler, A. J. Rossini, G. Sawitzki, C. Smith, G. Smyth, L. Tierney, J. Y. Yang, and J. Zhang. Bioconductor: open software development for computational biology and bioinformatics.Genome Biology, 5(10):R80, Sept. 2004. [ DOI | http ]
[9] L. N. Hutchins, S. M. Murphy, P. Singh, and J. H. Graber. Position-dependent motif characterization using non-negative matrix factorization.Bioinformatics, 24(23):2684-2690, Dec. 2008. [ DOI | http ]
[10] J. T. Leek and J. D. Storey. Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis.PLoS Genet, 3(9):e161, Sept. 2007. [ DOI | http ]
[11] S. Nik-Zainal, L. B. Alexandrov, D. C. Wedge, P. Van Loo, C. D. Greenman, K. Raine, D. Jones, J. Hinton, J. Marshall, L. A. Stebbings, A. Menzies, S. Martin, K. Leung, L. Chen, C. Leroy, M. Ramakrishna, R. Rance, K. W. Lau, L. J. Mudie, I. Varela, D. J. McBride, G. R. Bignell, S. L. Cooke, A. Shlien, J. Gamble, I. Whitmore, M. Maddison, P. S. Tarpey, H. R. Davies, E. Papaemmanuil, P. J. Stephens, S. McLaren, A. P. Butler, J. W. Teague, G. Jönsson, J. E. Garber, D. Silver, P. Miron, A. Fatima, S. Boyault, A. Langerød, A. Tutt, J. W. Martens, S. A. Aparicio, A. Borg, A. V. Salomon, G. Thomas, A.-L. Børresen-Dale, A. L. Richardson, M. S. Neuberger, P. A. Futreal, P. J. Campbell, and M. R. Stratton. Mutational Processes Molding the Genomes of 21 Breast Cancers.Cell, 149(5):979-993, May 2012. [ DOI | http ]
[12] V. Obenchain, M. Morgan, and M. Lawrence. VariantAnnotation: Annotation of Genetic Variants, 2011. [ .html ]
[13] W. Stacklies, H. Redestig, M. Scholz, D. Walther, and J. Selbig. pcaMethodsa bioconductor package providing PCA methods for incomplete data.Bioinformatics, 23(9):1164-1167, May 2007. [ DOI | http ]
[14] Y. Sun, N. R. Zhang, and A. B. Owen. Multiple hypothesis testing adjusted for latent variables, with an application to the AGEMAP gene expression data.The Annals of Applied Statistics, 6(4):1664-1688, Dec. 2012. Zentralblatt MATH identifier: 06141543; Mathematical Reviews number (MathSciNet): MR3058679. [ DOI | http ]
[15] H. Wickham.ggplot2: Elegant Graphics for Data Analysis. Springer, New York, 1st ed. 2009. corr. 3rd printing 2010 edition edition, Feb. 2010. [ http ]