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Issue No.03 - March (2012 vol.45)
pp: 39-46
Fabio Vandin , Brown University
Benjamin J. Raphael , Brown University
ABSTRACT
Two proposed algorithms predict which combinations of mutations in cancer genomes are priorities for experimental study. One relies on interaction network data to identify recurrently mutated sets of genes, while the other searches for groups of mutations that exhibit specific combinatorial properties.
INDEX TERMS
computational biology, bioinformatics, genome sequencing, cancer genomics, networks, diffusion processes, Markov chain Monte Carlo
CITATION
Fabio Vandin, Benjamin J. Raphael, "Algorithms and Genome Sequencing: Identifying Driver Pathways in Cancer", Computer, vol.45, no. 3, pp. 39-46, March 2012, doi:10.1109/MC.2012.71
REFERENCES
1. S.C. Schuster, "Next-Generation Sequencing Transforms Today's Biology," Nature Methods, Jan. 2008, pp. 16-18.
2. M. Meyerson, S. Gabriel, and G. Getz, "Advances in Understanding Cancer Genomes through Second-Generation Sequencing," Nature Reviews Genetics, Oct. 2010, pp. 685-696.
3. The Cancer Genome Atlas Research Network, "Integrated Genomic Analyses of Ovarian Carcinoma," Nature,30 June 2011, pp. 609-615.
4. G. Parmigiani et al., "Response to Comments on 'The Consensus Coding Sequences of Human Breast and Colorectal Cancers,'" Science,14 Sept. 2007, p. 1500.
5. N. Stransky et al., "The Mutational Landscape of Head and Neck Squamous Cell Carcinoma," Science,26 Aug. 2011, pp. 1157-1160.
6. Y. Benjamini and Y. Hochberg, "Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing," J. Royal Statistical Soc., Series B (Methodological), vol. 57, no. 1, 1995, pp. 289-300.
7. F. McCormick,"Signalling Networks That Cause Cancer," Trends in Cell Biology, Dec. 1999, pp. M53-M56.
8. F. Vandin, E. Upfal, and B.J. Raphael, "Algorithms for Detecting Significantly Mutated Pathways in Cancer," J. Computational Biology, Mar. 2011, pp. 507-522.
9. T. Ideker and R. Sharan, "Protein Networks in Disease," Genome Research, Apr. 2008, pp. 644-652.
10. F. Vandin, E. Upfal, and B.J. Raphael, "De Novo Discovery of Mutated Driver Pathways in Cancer," Genome Research, Feb. 2012, pp. 375-385.
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