REDEFINING CpG ISLANDS USING A HIDEEN MARKOV MODEL

[1]  A. Feinberg,et al.  A species-generalized probabilistic model-based definition of CpG islands , 2009, Mammalian Genome.

[2]  Rafael A. Irizarry,et al.  Genome-wide methylation analysis of human colon cancer reveals similar hypo- and hypermethylation at conserved tissue-specific CpG island shores , 2008, Nature Genetics.

[3]  T. Mikkelsen,et al.  Genome-scale DNA methylation maps of pluripotent and differentiated cells , 2008, Nature.

[4]  John M. Greally,et al.  CG dinucleotide clustering is a species-specific property of the genome , 2007, Nucleic acids research.

[5]  A. Feinberg.  Phenotypic plasticity and the epigenetics of human disease , 2007, Nature.

[6]  Wilfred W. Li,et al.  MEME: discovering and analyzing DNA and protein sequence motifs , 2006, Nucleic Acids Res..

[7]  Richard J Boys,et al.  A Bayesian Approach to DNA Sequence Segmentation , 2004, Biometrics.

[8]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[9]  Mark Hoebeke,et al.  Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models. , 2002, Nucleic acids research.

[10]  Daiya Takai,et al.  Comprehensive analysis of CpG islands in human chromosomes 21 and 22 , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[11]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[12]  R. Jaenisch,et al.  Development: DNA methylation in Drosophila melanogaster , 2000, Nature.

[13]  Sean R. Eddy,et al.  Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids , 1998 .

[14]  Michael Gribskov,et al.  Combining evidence using p-values: application to sequence homology searches , 1998, Bioinform..

[15]  Florence Muri,et al.  Modelling Bacterial Genomes Using Hidden Markov Models , 1998, COMPSTAT.

[16]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[17]  Lawrence R. Rabiner,et al.  A tutorial on hidden Markov models and selected applications in speech recognition , 1989, Proc. IEEE.

[18]  G. Churchill.  Stochastic models for heterogeneous DNA sequences. , 1989, Bulletin of mathematical biology.

[19]  M. Frommer,et al.  CpG islands in vertebrate genomes. , 1987, Journal of molecular biology.

[20]  A. Bird.  CpG-rich islands and the function of DNA methylation , 1986, Nature.