Review of signal processing in genetics

Fluctuation and Noise Letters

Volumn 5, Issue 4, 2005, Pages

  Berryman, M J ^a   Allison, A ^a   Wilkinson, C R ^a,b   Abbott, D ^a  

^a UNIVERSITY OF ADELAIDE   (Australia)

^b CHILD HEALTH RESEARCH INSTITUTE   (Australia)

Author keywords

Autocorrelation; DNA sequences; Hidden Markov models; Mutual information; Spectral analysis; Time series analysis

Indexed keywords

EID: 29144487926     PISSN: 02194775     EISSN: None     Source Type: Journal    
DOI: 10.1142/S021947750500294X     Document Type: Article

References (86)

1. Nature Genetics editorial team, Wag the dogma, Nature Genetics 30 (2002) 343-344.
2. L. H. Caporale, Darwin in the Genome: Molecular Strategies in Biological Evolution (McGraw-Hill, 2003).
3. P. Clerc and P. Avner, Role of the region 3' to xist exon 6 in the counting process of X-chromosome inactivation, Nature Genetics 19 (1998) 249-253.
4. J. S. Mattick, Non-coding RNAs: The architects of eukaryotic complexity, EMBO Reports 2 (2001) 986-991.
5. D. C. Boyd, A. Pombo and S. Murphy, Interaction of proteins with promoter elements the human U2 snRNA genes in vivo, Gene 315 (2003) 103-112.
6. G. P. Harmer, D. Abbott, P. G. Taylor and J. M. R. Parrondo, Brownian ratchets and Parrondo's games, Chaos 11 (2001) 705-714.
7. D. C. Rubinsztein, W. Amos, J. Leggo, S. Goodburn, R. S. Ramesar, J. Old, R. Bontrop, R. McMahon, D. E. Barton and M. A. Ferguson-Smith, Mutational bias provides a model for the evolution of Huntington's disease and predicts a general increase in disease prevalance, Nature Genetics 7 (1994) 525-530.
8. P. Worning, L. J. Jensen, K. E. Nelson, S. Brunak and D. W. Ussery, Structural analysis of DNA sequence: Evidence for lateral gene transfer, Thermotoga maritima, Nucleic Acids Res. 28 (2000) 706-709.
9. J. P. Fitch and B. Sokhansanj, Genomic engineering: Moving beyond DNA sequence to function, Proc. IEEE 88 (2000) 1949-1971.
10. D. Anastassiou, Genomic signal processing, IEEE Signal Processing Magazine 18 (2001) 8-20.
11. D. Anastassiou, Frequency-domain analysis of biomolecular sequences, Bioinformatics 16 (2000) 1073-1081.
12. Z. Yu, V. Anh and K. Lau, Measure representation and multifractal analysis of complete genomes, Physical Review E 64 (2001) 031903.
13. R. Durbin, S. Eddy, A. Krogh and G. Mitchison, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids (Cambridge University Press, 1998).
14. A. V. Lukashin and M. Borodovsky, GeneMark.hmm: New solutions for gene finding, Nucleic Acids Res. 26 (1998) 1107-1115.
15. X.-Y. Zhang, F. Chen, Y.-T. Zhang, S. C. Agner, M. Akay, Z.-H. Lu, M. M. Y. Waye and S.K.-W. Tsui, Signal processing techniques in genomic engineering, Proc. IEEE 90 (2002) 1822-1833.
16. B. N. Kholodenko, A. Kiyatkin, F. J. Bruggeman, E. Sontag, H. V. Westerhoff and J. B. Hoek, Untangling the wires: A strategy to trace functional interactions in signaling and gene networks, Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 12841-12846.
17. J. T. Tyson, K. C. Chen and B. Novak, Sniffers, buzzers, toggles and blinkers: Dynamics of regulatory and signaling pathways in the cell, Current Opinion in Cell Biology 15 (2003) 221-231.
18. M. Thattai and A. van Oudenaarden, Intrinsic noise in gene regulatory networks, Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 8614-8619.
19. A.-L. Barabási and Z. N. Oltvai, Network biology: Understanding the cell's functional organization, Nature Reviews Genetics 5 (2004) 101-113.
20. H. Kobayashi, M. Kærn, M. Araki, K. Chung, T. S. Gardner, C. R. Cantor and J. J. Collins, Programmable cells: Interfacing natural and engineered gene networks, Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 8414-8419.
21. J. Hasty, D. McMillen and J. J. Collins, Engineered gene circuits, Nature 420 (2002) 224-230.
22. E. M. Ozbudak, M. Thattai, I. Kurster, A. D. Grossman and A. van Oudenaarden, Regulation of noise in the expression of a single gene, Nature Genetics 31 (2002) 69-73.
23. W. H. Majoros, M. Pertea and S. L. Salzberg, Efficient implementation of a generalized pair hidden Markov model for comparative gene finding, Bioinformatics 21 (2005) 1782-1788.
24. N. von Öhsen, I. Sommer, R. Zimmer and T. Lengauer, Arby: Automatic protein structure prediction using profile-profile alignment and confidence measures, Bioinformatics 20 (2004) 2228-2235.
25. M. J. Berryman, A. Allison, P. Carpena and D. Abbott, Signal processing and statistical methods in analysis of text and DNA, in Proc. SPIE: Biomedical Applications of Micro- and Nanoengineering, ed. D. V. Nicolau, Vol. 4937 (2002), pp. 231-240.
26. M. J. Berryman, A. Allison and D. Abbott, Stochastic evolution and multifractal classification of prokaryotes, in Proc. of the SPIE: Fluctuations and Noise in Biological, Biophysical and Biomedical Systems, ed. S. M. Bezrukov, Vol. 5110 (2003), pp. 192-200.
27. M. Itoh, S. Goto, T. Akutsu and M. Kanehisa, Fast and accurate database homology search using upper bounds of local alignment scores, Bioinformatics 21 (2005) 912-921.
28. M. J. Berryman, A. Allison and D. Abbott, Mutual information for examining correlations in DNA, Fluctuation and Noise Letters 4 (2004) L237-L246.
29. S. Winters-Hilt, W. Vercoutere, V. S. DeGuzman, D. Deamer, M. Akeson and D. Haussler, Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules, Biophysical Journal 84 (2003) 967-976.
30. C. Bystroff, V. Thorsson and D. Baker, HMMSTR: A hidden Markov model for local sequence-structure correlations in proteins, Journal of Molecular Biology 301 (2000) 173-190.
31. B. Host, Better 1D predictions by experts with machines, Proteins: Structure, Function and Genetics S1 (1997) 192-197.
32. S. R. Eddy, HMMER: Profile hidden Markov models for biological sequence analysis (2001).
33. T. Hayashi, K. Makino, M. Ohnishi, K. Kurokawa, K. Ishii, K. Yokoyama et al., Complete genome sequence of enterohemorrhagic escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12, DNA Research 8 (2001) 11-22.
34. R. A. Welch, V. Burland, G. D. Plunkett, R. Redford, P. Roesch, D. Rasko et al., Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli, Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 17020-17024.
35. K. Putegowda, W. Worek, N. Pappas, A. Dandapani, P. Athanas and A. Dickerman, A run-time reconfigurable system for gene-sequence searching, in Proc. 16th International Conference on VLSI Design, IEEE Computer Society (2003), pp. 561-566.
36. D. Sussillo, A. Kundaje and D. Anastassiou, Spectrogram analysis of genomes, EURASIP Journal on Applied Signal Processing 2004 (2004) 29-42.
37. S. Tiwari, S. Ramachandran, A. Bhattacharya, S. Bhattacharya and R. Ramaswamy, Prediction of probable genes by Fourier analysis of genomic sequences, Computer Applications in Biosciences 13 (1997) 263-270.
38. P. P. Vaidyanathan and B.-J. Yoon, Gene and exon prediction using allpass-based filters, in Workshop on Genomic Signal Processing and Statistics (GENSIPS) (2002).
39. T. D. Read, S. N. Peterson, N. Tourasse, L. W. Baillie, I. T. Paulsen and K. E. Nelson et al., The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria, Nature 423 (2003) 81-86.
40. B. Audit, C. Vaillant, A. Arnéodo, Y. d'Aubenton Carafa and C. Thermes, Wavelet analysis of DNA bending profiles reveals structural constraints on the evolution of genomic sequences, Journal of Biological Physics 30 (2004) 33-81.
41. International Human Genome Sequencing Consortium, Initial sequencing and analysis of the human genome, Nature 409 (2001) 860-921.
42. W. Li, Mutual information functions versus correlation functions, Journal of Statistical Physics 60 (1990) 823-837.
43. P. Bernaolo-GalvÁn, P. Carpena, R. Román-Roldán and J. L. Oliver, Study of statistical correlations in DNA sequences, Gene 300 (2002) 105-115.
44. T. Higuchi, Approach to an irregular time series on the basis of the fractal theory, Physica D 31 (1988) 277-283.
45. D. Holste, I. Grosse and H. Herzel, Statistical analysis of the DNA sequence of human chromosome 22, Physical Review E 64 (2001) 041917.
46. D. Holste, I. Grosse, S. Beirer, P. Schieg and H. Herzel, Repeats and correlations in human DNA sequences, Physical Review E 67 (2003) 061913.
47. W. Li, The study of correlation structures of DNA sequences: A critical review, Computers and Chemistry 21 (1997) 257-271.
48. W. Li, Generating nontrivial long-range correlations and 1/f spectra by replication and mutation, International Journal of Bifurcation and Chaos 2 (1992) 137-154.
49. C.-K. Peng, S. V. Buldyrev, A. L. Goldberger, S. Havlin, F. Sciortino, M. Simon and H. E. Stanley, Long-range correlations in micleotide sequences, Nature 356 (1992) 168-170.
50. A. C. Frank and J. R. Lobry, Oriloc: Prediction of replication boundaries in unannotated bacterial chromosomes, Bioinformatics 16 (2000) 560-561.
51. P. D. Cristea, Large scale features in DNA genomic signals, Signal Processing 83 (2003) 871-888.
52. N. Chomsky, Three models for the description of language, IRE Transactions on Information Theory 2 (1956) 113-124.
53. N. Chomsky, On certain formal properties of grammars, Information and Control 2 (1959) 137-167.
54. S. Dong and D. B. Searls, Gene structure prediction by linguistic methods, Genomics 23 (1994) 540-551.
55. S. R. Eddy and R. Durbin, RNA sequence analysis using covariance models, Nucleic Acids Research 22 (1994) 2079-2088.
56. R. N. Mantegna, S. V. Buldyrev, A. L. Goldberger, S. Havlin, C.-K. Peng, M. Simons and H. E. Stanley, Linguistic features of non-coding DNA sequences, Physical Review Letters 73 (1994) 3169-3172.
57. R. N. Mantegna, S. V. Buldyrev, A. L. Goldberger, S. Havlin, C.-K. Peng, M. Simons and H. E. Stanley, Systematic analysis of coding and noncoding DNA sequences using methods of statistical linguistics, Physical Review E 52 (1995) 2939-2950.
58. R. N. Mantegna, S. V. Buldyrev, A. L. Goldberger, S. Havlin, C.-K. Peng, M. Simons and H. E. Stanley, Reply to comments on linguistic features of non-coding DNA sequences, Physical Review Letters 76 (1996) 1979-1981.
59. S. Small, A. Blair and M. Levine, Regulation of even-skipped stripe 2 in the Drosophila embryo, The EMBO Journal 11 (1992) 4047-4057.
60. P. Bucher and A. Bairoch, A generalized profile syntax for biomolecular sequences motifs and its function in automatic sequence interpretation, in Proc. 2nd International Conference on Intelligent Systems for Molecular Biology, eds. R. Altman, D. Brutlag, P. Karp, R. Lathrop and D. Searls (1994), pp. 53-61.
61. L. Falquet, M. Pagni, P. Bucher, N. Hulo, C. J. A. Sigrist, K. Hofmann and A. Bairoch, The PROSITE database, its status in 2002, Nucleic Acids Res. 30 (2002) 235-238.
62. M. Ortuño, P. Carpena, P. Bernaola-Galván, E. Muñoz and A. M. Somoza, Keyword detection in natural languages and DNA, Europhysics Letters 57 (2002) 759-764.
63. M. J. Berryman, A. Allison and D. Abbott, Statistical techniques for text classification based on word recurrence intervals, Fluctuations and Noise Letters 3 (2003) L1-L10.
64. B. M. E. Moret, J. Tang, L.-S. Wang and T. Warnow, Steps toward accurate reconstructions of phylogenies from gene-order data, Journal of Computer and Systems Sciences 65 (2002) 508-525.
65. R. Mutihac, A. Cicuttin and R. C. Mutihac, Entropic approach to information coding in DNA molecules, Materials Science and Engineering C 18 (2001) 51-60.
66. J. L. de Risi, V. R. Iyer and P. O. Brown, Exploring the metabolic and genetic control of gene expression on a genomic scale, Science 278 (1997) 680-686.
67. Y. H. Yang, M. J. Buckley, S. Dudoit and T. P. Speed, Comparison of methods for image analysis on cDNA microarray data, Journal of Computational and Graphical Statistics 11 (2002) 108-136.
68. C. H. Mastrangelo, M. A. Burns and D. T. Burke, Microfabricated devices for genetic diagnostics, Proc. IEEE 86 1769-1787.
69. M. J. Martinez, A. D. Aragon, A. L. Rodiguez, J. M. Weber, J. A. Timlin, M. B. Sinclair, D. M. Haaland and M. Werner-Washburne, Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays, Nucleic Acids Res. 31 (2003) e18:1-8.
70. G. K. Smyth and T. P. Speed, Normalization of cDNA microarray data, in Methods: Selecting Candidate Genes from DNA Array Screens: Application to Neuroscience Methods 31 (2003) 265-273.
71. D. L. Wilson, M. K. Buckley, C. A. Helliwell and I. W. Wilson, New normalization methods for cDNA microarray data, Bioinformatics 19 (2003) 1325-1332.
72. L. P. Zhao, R. Prentice and L. Breeden, Statistical modeling of large microarray data sets to identify stimulus-response profiles, Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 5631-5636.
73. S. C. Madeira and A. L. Oliveira, Biclustering algorithms for biological data analysis: A survey, IEEE Transactions on Computational Biology and Bioinformatics 1 (2004) 24-45.
74. N. Friedman, M. Linial, I. Nachman and D. Pe'er, Using Bayesian networks to analyze expression data, Journal of Computation Biology 7 (2000) 601-620.
75. Z. Bar-Joseph, G. Gerber, D. Gifford, T. Jaakkola and I. Simon, A new approach to analyzing gene expression time series data, in Proc. Sixth Annual International Conference on Research in Computational Molecular Biology (2002), pp. 39-48.
76. M. K. Kerr, M. Martin and G. A. Churchill, Analysis of variance for gene expression microarray data, Journal of Computational Biology 7 (2000) 819-837.
77. G. Balázsi, K. A. Kay, A. L. Barabási and Z. N. Oltvai, Spurious spatial periodicity of co-expression in microarray data due to printing design, Nucleic Acids Res. 31 (2003) 4425-4433.
78. J. A. Timlin, D. M. Haaland, M. B. Sinclair, A. D. Aragon, M. J. Martinez and M. Werner-Washburne, Hyperspectral microarray scanning: Impact on the accuracy and reliability of gene expression data, BMC Genomics 6 (2005).
79. G. F. V. Glonek and P. J. Solomon, Factorial and time course designs for cDNA microarray experiments, Biostatistics 5 (2004) 89-111.
80. P. Arena, L. Fortuna and L. Occhipinti, A CNN algorithm for real time analysis of DNA microarrays, IEEE Transactions on Circuits and Systems - I: Fundamental Theory and Applications 49 (2002) 335-340.
81. Y. Moreau, F. de Smet, G. Thijs, K. Marchal and B. de Moor, Functional bioinformatics of microarray data: From expression to regulation, Proc. IEEE 90 (2002) 1722-1743.
82. G. M. James and T. J. Hastie, Functional linear discriminant analysis for irregularly sampled curves, Journal of the Royal Statistical Society Series B 63 (2001) 533-550.
83. S. Kullback, Information Theory and Statistics (Dover Publications, 1968).
84. B. D. Silverman and R. Linsker, A measure of DNA periodicity, Journal of Theoretical Biology 118 (1986) 295-300.
85. S. Tavaré and B. W. Giddings, Mathematical Methods for DNA Sequences (CRC Press, 1989), pp. 117-131.
86. E. Coward, Equivalence of two Fourier methods for biological sequences, Journal of Mathematical Biology 36 (1997) 64-70.