Determining Coding CpG Islands by Identifying Regions Significant for Pattern Statistics on Markov Chains
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DOI: 10.2202/1544-6115.1677
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- Ryan Lister & Mattia Pelizzola & Robert H. Dowen & R. David Hawkins & Gary Hon & Julian Tonti-Filippini & Joseph R. Nery & Leonard Lee & Zhen Ye & Que-Minh Ngo & Lee Edsall & Jessica Antosiewicz-Bourg, 2009. "Human DNA methylomes at base resolution show widespread epigenomic differences," Nature, Nature, vol. 462(7271), pages 315-322, November.
- Nuel Gregory, 2006. "Numerical Solutions for Patterns Statistics on Markov Chains," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 5(1), pages 1-45, October.
- Vergne Nicolas, 2008. "Drifting Markov Models with Polynomial Drift and Applications to DNA Sequences," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 7(1), pages 1-45, February.
- Hsieh Fushing & Chen Shu-Chun & Pollard Katherine, 2009. "A Nearly Exhaustive Search for CpG Islands on Whole Chromosomes," The International Journal of Biostatistics, De Gruyter, vol. 5(1), pages 1-24, May.
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Keywords
Markov chains; pattern statistics; CpG islands; genomics;All these keywords.
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