Statistical methods for detecting periodic fragments in DNA sequence data
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Julien Epps | Hua Ying | Gavin A Huttley | J. Epps | G. Huttley | H. Ying
[1] Robert Boorstyn,et al. Single tone parameter estimation from discrete-time observations , 1974, IEEE Trans. Inf. Theory.
[2] Sanjit K. Mitra,et al. Power spectrum analysis for DNA sequences , 2003, Seventh International Symposium on Signal Processing and Its Applications, 2003. Proceedings..
[3] Alfonso G. Fernandez,et al. Nucleosome positioning determinants. , 2007, Journal of molecular biology.
[4] Steven A. Tretter,et al. Estimating the frequency of a noisy sinusoid by linear regression , 1985, IEEE Trans. Inf. Theory.
[5] E. Ambikairajah,et al. An integer period DFT for biological sequence processing , 2008, 2008 IEEE International Workshop on Genomic Signal Processing and Statistics.
[6] E. Trifonov,et al. The pitch of chromatin DNA is reflected in its nucleotide sequence. , 1980, Proceedings of the National Academy of Sciences of the United States of America.
[7] A. Mclachlan,et al. Fourteen actin-binding sites on tropomyosin? , 1975, Nature.
[8] Hanspeter Herzel,et al. Interpreting correlations in biosequences , 1998 .
[9] R. Linsker,et al. A measure of DNA periodicity. , 1986, Journal of theoretical biology.
[10] Steven M. Johnson,et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. , 2008, Genome research.
[11] Ronald W. Davis,et al. A high-resolution atlas of nucleosome occupancy in yeast , 2007, Nature Genetics.
[12] H. Drew,et al. Sequence periodicities in chicken nucleosome core DNA. , 1986, Journal of molecular biology.
[13] William A. Sethares,et al. Periodicity transforms , 1999, IEEE Trans. Signal Process..
[14] S. Karlin,et al. Comparative DNA analysis across diverse genomes. , 1998, Annual review of genetics.
[15] E N Trifonov,et al. Sequence Structure of Hidden 10.4-base Repeat in the Nucleosomes of C. elegans , 2008, Journal of biomolecular structure & dynamics.
[16] Irene K. Moore,et al. A genomic code for nucleosome positioning , 2006, Nature.
[17] Stephen J Freeland,et al. A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes , 2001, Genome Biology.
[18] H. Hartley,et al. Tests of significance in harmonic analysis. , 1949, Biometrika.
[19] S. Lonardi,et al. Supplemental Material to : Nucleosome landscape and control of transcription in the human malaria parasite , 2009 .
[20] G Bernardi,et al. Isochores and the evolutionary genomics of vertebrates. , 2000, Gene.
[21] T. Richmond,et al. Crystal structure of the nucleosome core particle at 2.8 Å resolution , 1997, Nature.
[22] A. Mclachlan,et al. The 14-fold periodicity in α-tropomyosin and the interaction with actin , 1976 .
[23] E. Dougherty,et al. Genomic Signal Processing and Statistics , 2005 .
[24] Edward N. Trifonov,et al. Repertoires of the Nucleosome-Positioning Dinucleotides , 2009, PloS one.
[25] E V Korotkov,et al. Method revealing latent periodicity of the nucleotide sequences modified for a case of small samples. , 1999, DNA research : an international journal for rapid publication of reports on genes and genomes.
[26] Julien Epps. A Hybrid Technique for the Periodicity Characterization of Genomic Sequence Data , 2009, EURASIP J. Bioinform. Syst. Biol..
[27] Stephan C. Schuster,et al. Nucleosome organization in the Drosophila genome , 2008, Nature.
[28] Thomas W. Parks,et al. Orthogonal, exactly periodic subspace decomposition , 2003, IEEE Trans. Signal Process..
[29] Korbinian Strimmer,et al. Identifying periodically expressed transcripts in microarray time series data , 2008, Bioinform..
[30] Avinash Bhandoola,et al. Biology Direct , 2006 .
[31] A. Mclachlan,et al. The 14-fold periodicity in alpha-tropomyosin and the interaction with actin. , 1976, Journal of Molecular Biology.
[32] Christopher J. R. Illingworth,et al. Criteria for confirming sequence periodicity identified by Fourier transform analysis: application to GCR2, a candidate plant GPCR? , 2008, Biophysical chemistry.
[33] Wentian Li,et al. The Study of Correlation Structures of DNA Sequences: A Critical Review , 1997, Comput. Chem..
[34] Matthias E. Futschik,et al. DNA Motifs and Sequence Periodicities , 2006, Silico Biol..
[35] P. Vandergheynst,et al. Fourier and wavelet transform analysis, a tool for visualizing regular patterns in DNA sequences. , 2000, Journal of theoretical biology.
[36] Guo-Cheng Yuan,et al. Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion , 2007, PLoS Comput. Biol..
[37] J. Widom. Short-range order in two eukaryotic genomes: relation to chromosome structure. , 1996, Journal of molecular biology.
[38] R. Voss,et al. Evolution of long-range fractal correlations and 1/f noise in DNA base sequences. , 1992, Physical review letters.
[39] C. Peng,et al. Long-range correlations in nucleotide sequences , 1992, Nature.
[40] Hua Ying,et al. Evidence that Localized Variation in Primate Sequence Divergence Arises from an Influence of Nucleosome Placement on DNA Repair , 2009, Molecular biology and evolution.
[41] D. Raup,et al. Periodicity of extinctions in the geologic past. , 1984, Proceedings of the National Academy of Sciences of the United States of America.
[42] Ronald K. Pearson,et al. BMC Bioinformatics BioMed Central Methodology article , 2005 .
[43] V. Chechetkin,et al. Search of hidden periodicities in DNA sequences. , 1995, Journal of theoretical biology.
[44] Cizhong Jiang,et al. Nucleosome positioning and gene regulation: advances through genomics , 2009, Nature Reviews Genetics.
[45] Andrey A. Ptitsyn,et al. Permutation test for periodicity in short time series data , 2006, BMC Bioinformatics.
[46] William A. Sethares,et al. Latent Periodicities in Genome Sequences , 2008, IEEE Journal of Selected Topics in Signal Processing.