Table of Contents
ISRN Bioinformatics
Volume 2013 (2013), Article ID 174064, 9 pages
http://dx.doi.org/10.1155/2013/174064
Research Article

NucVoter: A Voting Algorithm for Reliable Nucleosome Prediction Using Next-Generation Sequencing Data

Institute of Molecular Medicine and Genetics, Georgia Regents University, Augusta, GA 30912, USA

Received 17 July 2013; Accepted 8 September 2013

Academic Editors: A. Bolshoy, B. Haubold, S. Liuni, A. Pulvirenti, and C.-A. Tsai

Copyright © 2013 Boseon Byeon. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. J. C. Rajapakse and S. L. Ho, “Markov/neural model for Eukaryotic promoter recognition,” in Machine Learning in Bioinformatics, Y. Zhang and J. C. Rajapakse, Eds., pp. 283–299, John Wiley & Sons, New York, NY, USA, 2009. View at Google Scholar
  2. S. Draghici, Statistics and Data Analysis for Microarrays Using R and Bioconductor, CRC Press, New York, NY, USA, 2012.
  3. C. Jiang and B. F. Pugh, “Nucleosome positioning and gene regulation: advances through genomics,” Nature Reviews Genetics, vol. 10, no. 3, pp. 161–172, 2009. View at Publisher · View at Google Scholar · View at Scopus
  4. F. Zambelli and G. Pavesi, “Algorithmic issues in the analysis of Chip-seq data,” in Algorithms in Computational Molecular Biology, M. Elloumi and A. Y. Zomaya, Eds., pp. 425–448, John Wiley & Sons, New York, NY, USA, 2011. View at Google Scholar
  5. L. Bai and A. V. Morozov, “Gene regulation by nucleosome positioning,” Trends in Genetics, vol. 26, no. 11, pp. 476–483, 2010. View at Publisher · View at Google Scholar · View at Scopus
  6. O. Bell, V. K. Tiwari, N. H. Thomä, and D. Schübeler, “Determinants and dynamics of genome accessibility,” Nature Reviews Genetics, vol. 12, no. 8, pp. 554–564, 2011. View at Publisher · View at Google Scholar · View at Scopus
  7. G. Felsenfeld and M. Groudine, “Controlling the double helix,” Nature, vol. 421, no. 6921, pp. 448–453, 2003. View at Publisher · View at Google Scholar · View at Scopus
  8. K. Cui and K. Zhao, “Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq,” Methods in Molecular Biology, vol. 833, pp. 413–419, 2012. View at Publisher · View at Google Scholar · View at Scopus
  9. W. J. Ansorge, “Next-generation DNA sequencing techniques,” New Biotechnology, vol. 25, no. 4, pp. 195–203, 2009. View at Publisher · View at Google Scholar · View at Scopus
  10. X. Zhou, L. Ren, Q. Meng, Y. Li, Y. Yu, and J. Yu, “The next-generation sequencing technology and application,” Protein and Cell, vol. 1, no. 6, pp. 520–536, 2010. View at Publisher · View at Google Scholar · View at Scopus
  11. M. L. Eaton, K. Galani, S. Kang, S. P. Bell, and D. M. MacAlpine, “Conserved nucleosome positioning defines replication origins,” Genes and Development, vol. 24, no. 8, pp. 748–753, 2010. View at Publisher · View at Google Scholar · View at Scopus
  12. R. M. Fraser, D. Keszenman-Pereyra, M. W. Simmen, and J. Allan, “High-resolution mapping of sequence-directed nucleosome positioning on genomic DNA,” Journal of Molecular Biology, vol. 390, no. 2, pp. 292–305, 2009. View at Publisher · View at Google Scholar · View at Scopus
  13. N. Ponts, E. Y. Harris, J. Prudhomme et al., “Nucleosome landscape and control of transcription in the human malaria parasite,” Genome Research, vol. 20, no. 2, pp. 228–238, 2010. View at Publisher · View at Google Scholar · View at Scopus
  14. S. Shivaswamy, A. Bhinge, Y. Zhao, S. Jones, M. Hirst, and V. R. Iyer, “Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation,” PLoS Biology, vol. 6, no. 3, article e65, 2008. View at Publisher · View at Google Scholar · View at Scopus
  15. I. Albert, S. Wachi, C. Jiang, and B. F. Pugh, “GeneTrack—a genomic data processing and visualization framework,” Bioinformatics, vol. 24, no. 10, pp. 1305–1306, 2008. View at Publisher · View at Google Scholar · View at Scopus
  16. A. Nellore, K. Bobkov, E. Howe, A. Pankov, A. Diaz, and J. S. Song, “NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data,” Frontiers in Genetics, vol. 3, article 320, 2013. View at Google Scholar
  17. A. Weiner, A. Hughes, M. Yassour, O. J. Rando, and N. Friedman, “High-resolution nucleosome mapping reveals transcription-dependent promoter packaging,” Genome Research, vol. 20, no. 1, pp. 90–100, 2010. View at Publisher · View at Google Scholar · View at Scopus
  18. I. H. Witten and E. Frank, Data Mining, Morgan Kaufmann Publishers, 2005.
  19. O. Flores and M. Orozco, “nucleR: a package for non-parametric nucleosome positioning,” Bioinformatics, vol. 27, no. 15, Article ID btr345, pp. 2149–2150, 2011. View at Publisher · View at Google Scholar · View at Scopus
  20. J. Pevsner, Bioinformatics and Functional Genomics, John Wiley & Sons, New York, NY, USA, 2009.
  21. D. W. Huang, B. T. Sherman, and R. A. Lempicki, “Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists,” Nucleic Acids Research, vol. 37, no. 1, pp. 1–13, 2009. View at Publisher · View at Google Scholar · View at Scopus
  22. M. D. Robinson, J. Grigull, N. Mohammad, and T. R. Hughes, “FunSpec: a web-based cluster interpreter for yeast,” BMC Bioinformatics, vol. 3, article 35, 2002. View at Publisher · View at Google Scholar · View at Scopus