This Article 
   
 Share 
   
 Bibliographic References 
   
 Add to: 
 
Digg
Furl
Spurl
Blink
Simpy
Google
Del.icio.us
Y!MyWeb
 
 Search 
   
Algorithms and Genome Sequencing: Identifying Driver Pathways in Cancer
March 2012 (vol. 45 no. 3)
pp. 39-46
Fabio Vandin, Brown University
Eli Upfal, Brown University
Benjamin J. Raphael, Brown University
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.

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.

Index Terms:
computational biology, bioinformatics, genome sequencing, cancer genomics, networks, diffusion processes, Markov chain Monte Carlo
Citation:
Fabio Vandin, Eli Upfal, 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
Usage of this product signifies your acceptance of the Terms of Use.