Wavelet-based method to disentangle transcription- and replication-associated strand asymmetries in mammalian genomes

Applied and Computational Harmonic Analysis

Volumn 28, Issue 2, 2010, Pages 150-170

  Baker, Antoine ^a,b   Nicolay, Samuel ^c   Zaghloul, Lamia ^a,b   d'Aubenton Carafa, Yves ^b   Thermes, Claude ^b   Audit, Benjamin ^a,b   Arneodo, Alain ^a,b  

^a UNIVERSITÉ DE LYON   (France)

^b CNRS   (France)

^c UNIVERSITY OF LIÈGE   (Belgium)

Author keywords

Continuous wavelet transform; DNA sequences; Mammalian genomes; Replication; Strand compositional asymmetry; Transcription

Indexed keywords

ANALYZING WAVELETS; CHARACTERISTIC SIZE; COMPARATIVE ANALYSIS; CONTINUOUS WAVELET TRANSFORM; DNA DOUBLE HELICES; DNA STRANDS; GENE ORGANIZATION; GENOME EVOLUTION; HUMAN AUTOSOMES; HUMAN CHROMOSOMES; HUMAN GENES; HUMAN GENOMES; LARGE AMPLITUDE; LEAST-SQUARE FITTING; MAMMALIAN GENOMES; MULTISCALES; REPLICATION ORIGIN; TRANSCRIPTIONAL ACTIVITY; WAVELET-BASED METHODS;

CHROMATOGRAPHIC ANALYSIS; DNA; DNA SEQUENCES; GENES; MAMMALS; PATTERN RECOGNITION; WAVELET TRANSFORMS;

TRANSCRIPTION;

EID: 76149113227     PISSN: 10635203     EISSN: 1096603X     Source Type: Journal    
DOI: 10.1016/j.acha.2009.10.003     Document Type: Article

References (147)

1. Anglana M., Apiou F., Bensimon A., and Debatisse M. Dynamics of DNA replication in mammalian somatic cells: Nucleotide pool modulates origin choice and interorigin spacing. Cell 114 3 (2003) 385-394
2. Arneodo A., Argoul F., Bacry E., Elezgaray J., Freysz E., Grasseau G., Muzy J.-F., and Pouligny B. Wavelet transform of fractals. Wavelets and Applications (1992), Springer, Berlin 286-352
3. Arneodo A., Argoul F., Bacry E., Elezgaray J., and Muzy J.-F. Ondelettes, Multifractales et Turbulences : de l'ADN aux Croissances Cristallines (1995), Diderot Editeur, Arts et Sciences, Paris
4. Arneodo A., Argoul F., Bacry E., Muzy J.-F., and Tabard M. Golden mean arithmetic in the fractal branching of diffusion-limited aggregates. Phys. Rev. Lett. 68 23 (1992) 3456-3459
5. Arneodo A., Argoul F., Elezgaray J., and Grasseau G. Wavelet transform analysis of fractals: Application to nonequilibrium phase transitions. In: Turchetti G. (Ed). Nonlinear Dynamics (1989), World Scientific, Singapore 130-180
6. Arneodo A., Argoul F., Muzy J.-F., and Tabard M. Structural 5-fold symmetry in the fractal morphology of diffusion-limited aggregates. Physica A 188 1-3 (1992) 217-242
7. Arneodo A., Argoul F., Muzy J.-F., and Tabard M. Uncovering Fibonacci sequences in the fractal morphology of diffusion-limited aggregates. Phys. Lett. A 171 1-2 (1992) 31-36
8. A. Arneodo, B. Audit, E.-B. Brodie of Brodie, S. Nicolay, M. Touchon, Y. d'Aubenton-Carafa, M. Huvet, C. Thermes, Fractals and wavelets: What can we learn on transcription and replication from wavelet-based multifractal analysis of DNA sequences?, in: Encyclopedia of Complexity and System Science, 2008, in press
9. Arneodo A., Audit B., Decoster N., Muzy J.-F., and Vaillant C. Wavelet based multifractal formalism: Application to DNA sequences, satellite images of the cloud structure and stock market data. The Science of Disasters: Climate Disruptions, Heart Attacks, and Market Crashes (2002), Springer Verlag, Berlin 26-102
10. Arneodo A., Audit B., Faivre-Moskalenko C., Moukhtar J., Vaillant C., Argoul F., d'Aubenton-Carafa Y., and Thermes C. From DNA sequence to chromatin organization: The fundamental role of genomic long-range correlations. Bull. Acad. Roy. Belg. Mém. Cl. Sci. Collect. 8 Sér. 3 XXVIII 2049 (2008)
11. Arneodo A., Bacry E., Graves P.V., and Muzy J.-F. Characterizing long-range correlations in DNA sequences from wavelet analysis. Phys. Rev. Lett. 74 16 (1995) 3293-3296
12. Arneodo A., Bacry E., and Muzy J.-F. The thermodynamics of fractals revisited with wavelets. Physica A 213 1-2 (1995) 232-275
13. Arneodo A., d'Aubenton-Carafa Y., Audit B., Bacry E., Muzy J.-F., and Thermes C. Nucleotide composition effects on the long-range correlations in human genes. Eur. Phys. J. B 1 2 (1998) 259-263
14. Arneodo A., d'Aubenton-Carafa Y., Audit B., Brodie of Brodie E.-B., Nicolay S., St-Jean P., Thermes C., Touchon M., and Vaillant C. DNA in chromatin: From genome-wide sequence analysis to the modeling of replication in mammals. Adv. Chem. Phys. 135 (2007) 203-252
15. Arneodo A., d'Aubenton-Carafa Y., Bacry E., Graves P.V., Muzy J.-F., and Thermes C. Wavelet based fractal analysis of DNA sequences. Physica D 96 1-4 (1996) 291-320
16. Arneodo A., Decoster N., Kestener P., and Roux S.G. A wavelet-based method for multifractal image analysis: From theoretical concepts to experimental applications. Adv. Imaging Electr. Phys. 126 (2003) 1-92
17. Arneodo A., Decoster N., and Roux S.G. Intermittency, log-normal statistics, and multifractal cascade process in high-resolution satellite images of cloud structure. Phys. Rev. Lett. 83 6 (1999) 1255-1258
18. Arneodo A., Decoster N., and Roux S.G. A wavelet-based method for multifractal image analysis. I. Methodology and test applications on isotropic and anisotropic random rough surfaces. Eur. Phys. J. B 15 3 (2000) 567-600
19. Arneodo A., Grasseau G., and Holschneider M. Wavelet transform of multifractals. Phys. Rev. Lett. 61 20 (1988) 2281-2284
20. Arneodo A., Manneville S., and Muzy J.-F. Towards log-normal statistics in high Reynolds number turbulence. Eur. Phys. J. B 1 1 (1998) 129-140
21. Arneodo A., Manneville S., Muzy J.-F., and Roux S.G. Revealing a lognormal cascading process in turbulent velocity statistics with wavelet analysis. Philos. Trans. R. Soc. Lond. A 357 1760 (1999) 2415-2438
22. Arneodo A., Muzy J.-F., and Sornette D. "Direct" causal cascade in the stock market. Eur. Phys. J. B 2 2 (1998) 277-282
23. Arrault J., Arneodo A., Davis A., and Marshak A. Wavelet based multifractal analysis of rough surfaces: Application to cloud models and satellite data. Phys. Rev. Lett. 79 1 (1997) 75-78
24. Audit B., Nicolay S., Huvet M., Touchon M., d'Aubenton-Carafa Y., Thermes C., and Arneodo A. DNA replication timing data corroborate in silico human replication origin predictions. Phys. Rev. Lett. 99 24 (2007) 248102
25. Audit B., Thermes C., Vaillant C., d'Aubenton-Carafa Y., Muzy J.-F., and Arneodo A. Long-range correlations in genomic DNA: A signature of the nucleosomal structure. Phys. Rev. Lett. 86 11 (2001) 2471-2474
26. Audit B., Vaillant C., Arneodo A., d'Aubenton-Carafa Y., and Thermes C. Long-range correlations between DNA bending sites: Relation to the structure and dynamics of nucleosomes. J. Mol. Biol. 316 4 (2002) 903-918
27. Audit B., Zaghloul L., Vaillant C., Chevereau G., d'Aubenton-Carafa Y., Thermes C., and Arneodo A. Open chromatin encoded in DNA sequence is the signature of "master" replication origins in human cells. Nucl. Acids Res. 37 18 (2009) 6064-6075
28. Azbel' M.Y. Universality in a DNA statistical structure. Phys. Rev. Lett. 75 1 (1995) 168-171
29. Bacry E., Muzy J.-F., and Arneodo A. Singularity spectrum of fractal signals from wavelet analysis: Exact results. J. Stat. Phys. 70 (1993) 635-674
30. Beletskii A., Grigoriev A., Joyce S., and Bhagwat A.S. Mutations induced by bacteriophage T7 RNA polymerase and their effects on the composition of the T7 genome. J. Mol. Biol. 300 5 (2000) 1057-1065
31. Bell S.P., and Dutta A. DNA replication in eukaryotic cells. Annu. Rev. Biochem. 71 (2002) 333-374
32. Bernardi G. Isochores and the evolutionary genomics of vertebrates. Gene 241 1 (2000) 3-17
33. Bogan J.A., Natale D.A., and Depamphilis M.L. Initiation of eukaryotic DNA replication: Conservative or liberal?. J. Cell. Physiol. 184 2 (2000) 139-150
34. α spectrum in DNA sequences. Europhys. Lett. 23 6 (1993) 389-394
35. Brodie of Brodie E.-B., Nicolay S., Touchon M., Audit B., d'Aubenton-Carafa Y., Thermes C., and Arneodo A. From DNA sequence analysis to modeling replication in the human genome. Phys. Rev. Lett. 94 24 (2005) 248103
36. Buldyrev S.V., Goldberger A.L., Havlin S., Mantegna R.N., Matsa M.E., Peng C.-K., Simons M., and Stanley H.E. Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis. Phys. Rev. E 51 5 (1995) 5084-5091
37. Bulmer M. Strand symmetry of mutation rates in the beta-globin region. J. Mol. Evol. 33 4 (1991) 305-310
38. Caddle L.B., Grant J.L., Szatkiewicz J., van Hase J., Shirley B.-J., Bewersdorf J., Cremer C., Arneodo A., Khalil A., and Mills K.D. Chromosome neighborhood composition determines translocation outcomes after exposure to high-dose radiation in primary cells. Chrom. Res. 15 8 (2007) 1061-1073
39. Cadoret J.-C., Meisch F., Hassan-Zadeh V., Luyten I., Guillet C., Duret L., Quesneville H., and Prioleau M.-N. Genome-wide studies highlight indirect links between human replication origins and gene regulation. Proc. Natl. Acad. Sci. USA 105 41 (2008) 15837-15842
40. Chargaff E. Structure and function of nucleic acids as cell constituents. Fed. Proc. 10 3 (1951) 654-659
41. Chatzidimitriou-Dreismann C.A., and Larhammar D. Long-range correlations in DNA. Nature 361 6409 (1993) 212-213
42. In: Combes J., Grossmann A., and Tchamitchian P. (Eds). Wavelets (1989), Springer, Berlin
43. Coverley D., and Laskey R.A. Regulation of eukaryotic DNA replication. Annu. Rev. Biochem. 63 (1994) 745-776
44. Daubechies I. Ten Lectures on Wavelets (1992), SIAM, Philadelphia
45. Decoster N., Roux S.G., and Arneodo A. A wavelet-based method for multifractal image analysis. II. Applications to synthetic multifractal rough surfaces. Eur. Phys. J. B 15 4 (2000) 739-764
46. Delour J., Muzy J.-F., and Arneodo A. Intermittency of 1D velocity spatial profiles in turbulence: A magnitude cumulant analysis. Eur. Phys. J. B 23 2 (2001) 243-248
47. Demeret C., Vassetzky Y., and Méchali M. Chromatin remodelling and DNA replication: From nucleosomes to loop domains. Oncogene 20 24 (2001) 3086-3093
48. Duret L. Evolution of synonymous codon usage in metazoans. Curr. Opin. Genet. Dev. 12 6 (2002) 640-649
49. In: Erlebacher G., Hussaini M., and Jameson L. (Eds). Wavelets: Theory and Applications (1996), Oxford University Press, Oxford
50. In: Farge M., Hunt J., and Vassilicos J. (Eds). Wavelets, Fractals and Fourier (1996), Clarendon Press, Oxford
51. Fickett J.W., Torney D.C., and Wolf D.R. Base compositional structure of genomes. Genomics 13 4 (1992) 1056-1064
52. Fisher D., and Méchali M. Vertebrate HoxB gene expression requires DNA replication. EMBO J. 22 14 (2003) 3737-3748
53. Francino M.P., and Ochman H. Strand symmetry around the beta-globin origin of replication in primates. Mol. Biol. Evol. 17 3 (2000) 416-422
54. Francino M.P., and Ochman H. Deamination as the basis of strand-asymmetric evolution in transcribed Escherichia coli sequences. Mol. Biol. Evol. 18 6 (2001) 1147-1150
55. Frank A.C., and Lobry J.R. Asymmetric substitution patterns: A review of possible underlying mutational or selective mechanisms. Gene 238 1 (1999) 65-77
56. Freeman J.M., Plasterer T.N., Smith T.F., and Mohr S.C. Patterns of genome organization in bacteria. Science 279 (1998) 1827
57. Gardiner K. Base composition and gene distribution: Critical patterns in mammalian genome organization. Trends Genet. 12 12 (1996) 519-524
58. Gerbi S.A., and Bielinsky A.K. DNA replication and chromatin. Curr. Opin. Genet. Dev. 12 2 (2002) 243-248
59. Gierlik A., Kowalczuk M., Mackiewicz P., Dudek M.R., and Cebrat S. Is there replication-associated mutational pressure in the Saccharomyces cerevisiae genome?. J. Theor. Biol. 202 4 (2000) 305-314
60. Gilbert D.M. Making sense of eukaryotic DNA replication origins. Science 294 5540 (2001) 96-100
61. Gilbert D.M. In search of the holy replicator. Nat. Rev. Mol. Cell Biol. 5 10 (2004) 848-855
62. Goupillaud P., Grossmann A., and Morlet J. Cycle-octave and related transforms in seismic signal analysis. Geoexploration 23 (1984) 85-102
63. Green P., Ewing B., Miller W., Thomas P.J., and Green E.D. Transcription-associated mutational asymmetry in mammalian evolution. Nat. Genet. 33 4 (2003) 514-517
64. Grossmann A., and Morlet J. Decomposition of Hardy functions into square integrable wavelets of constant shape. SIAM J. Math. Anal. 15 (1984) 723-736
65. Grossmann A., and Morlet J. Decomposition of functions into wavelets of constant shape and related transforms. In: Streit L. (Ed). Mathematics and Physics, Lectures on Recent Results (1985), World Scientific 135-165
66. Hentschel H.G.E. Stochastic multifractality and universal scaling distributions. Phys. Rev. E 50 1 (1994) 243-261
67. Herzel H., and Große I. Measuring correlations in symbol sequences. Physica A 216 4 (1995) 518-542
68. Holschneider M. On the wavelet transform of fractal objects. J. Stat. Phys. 50 (1988) 963-993
69. Holschneider M., and Tchamitchian P. Régularité locale de la fonction non-différentiable de Riemann. In: Lemarié P.G. (Ed). Les Ondelettes en 1989 (1990), Springer, Berlin 102-124
70. Huvet M., Nicolay S., Touchon M., Audit B., d'Aubenton-Carafa Y., Arneodo A., and Thermes C. Human gene organization driven by the coordination of replication and transcription. Genome Res. 17 9 (2007) 1278-1285
71. Hyrien O., and Méchali M. Chromosomal replication initiates and terminates at random sequences but at regular intervals in the ribosomal DNA of Xenopus early embryos. EMBO J. 12 12 (1993) 4511-4520
72. Ivanov P.C., Amaral L.A., Goldberger A.L., Havlin S., Rosenblum M.G., Struzik Z.R., and Stanley H.E. Multifractality in human heartbeat dynamics. Nature 399 6735 (1999) 461-465
73. Ivanov P.C., Rosenblum M.G., Peng C.K., Mietus J., Havlin S., Stanley H.E., and Goldberger A.L. Scaling behaviour of heartbeat intervals obtained by wavelet-based time-series analysis. Nature 383 6598 (1996) 323-327
74. Jacob F., Brenner S., and Cuzin F. On the regulation of DNA replication in bacteria. Cold Spring Harb. Symp. Quant. Biol. 28 (1963) 329-342
75. Jaffard S. Hölder exponents at given points and wavelet coefficients. C. R. Acad. Sci. Paris Sér. I 308 4 (1989) 79-81
76. Jaffard S. Pointwise smoothness, two-microlocalization and wavelet coefficients. Publ. Mat. 35 (1991) 155-168
77. Jaffard S. Multifractal formalism for functions, Part I: Results valid for all functions. SIAM J. Math. Anal. 28 4 (1997) 944-970
78. Jaffard S. Multifractal formalism for functions, Part II: Self-similar functions. SIAM J. Math. Anal. 28 4 (1997) 971-998
79. Jaffard S., Lashermes B., and Abry P. Wavelet leaders in multifractal analysis. In: Qian T., Vai M.I., and Xu Y. (Eds). Wavelet Analysis and Applications (2006), Birkhäuser Verlag, Basel, Switzerland 219-264
80. In: Jaffard S., Meyer Y., and Ryan R. (Eds). Wavelets: Tools for Science and Technology (2001), SIAM, Philadelphia
81. Karlin S., and Brendel V. Patchiness and correlations in DNA sequences. Science 259 5095 (1993) 677-680
82. Kestener P., and Arneodo A. Three-dimensional wavelet-based multifractal method: The need for revisiting the multifractal description of turbulence dissipation data. Phys. Rev. Lett. 91 19 (2003) 194501
83. Kestener P., and Arneodo A. Generalizing the wavelet-based multifractal formalism to random vector fields: Application to three-dimensional turbulence velocity and vorticity data. Phys. Rev. Lett. 93 4 (2004) 044501
84. Kestener P., and Arneodo A. A multifractal formalism for vector-valued random fields based on wavelet analysis: Application to turbulent velocity and vorticity 3D numerical data. Stoch. Environ. Res. Risk Assess. 22 (2007) 421
85. Kestener P., Lina J.-M., Saint-Jean P., and Arneodo A. Wavelet-based multifractal formalism to assist in diagnosis in digitized mammograms. Image Anal. Stereol. 20 (2001) 169-174
86. Khalil A., Grant J., Caddle L., Atzema E., Mills K., and Arneodo A. Chromosome territories have a highly non-spherical morphology and non-random positioning. Chrom. Res. 15 (2007) 889-916
87. I features. II. Wavelet-based multifractal formalism. Astrophys. J. Suppl. Ser. 165 2 (2006) 512-550
88. Kuhn A., Argoul F., Muzy J.-F., and Arneodo A. Structural-analysis of electroless deposits in the diffusion-limited regime. Phys. Rev. Lett. 73 22 (1994) 2998-3001
89. Larhammar D., and Chatzidimitriou-Dreismann C.A. Biological origins of long-range correlations and compositional variations in DNA. Nucl. Acids Res. 21 22 (1993) 5167-5170
90. Lee T.I., Jenner R.G., Boyer L.A., Guenther M.G., Levine S.S., Kumar R.M., Chevalier B., Johnstone S.E., Cole M.F., Isono K., Koseki H., Fuchikami T., Abe K., Murray H.L., Zucker J.P., Yuan B., Bell G.W., Herbolsheimer E., Hannett N.M., Sun K., Odom D.T., Otte A.P., Volkert T.L., Bartel D.P., Melton D.A., Gifford D.K., Jaenisch R., and Young R.A. Control of developmental regulators by polycomb in human embryonic stem cells. Cell 125 2 (2006) 301-313
91. Li W. Generating non trivial long-range correlations and 1 / f spectra by replication and mutation. Int. J. Bifurc. Chaos 2 (1992) 137-154
92. Li W. The study of correlation structures of DNA sequences: A critical review. Comput. Chem. 21 4 (1997) 257-271
93. Li W.T., Marr T.G., and Kaneko K. Understanding long-range correlations in DNA-sequences. Physica D 75 1-3 (1994) 392-416
94. Li W., Stolovitzky G., Bernaola-Galván P., and Oliver J.L. Compositional heterogeneity within, and uniformity between, DNA sequences of yeast chromosomes. Genome Res. 8 9 (1998) 916-928
95. Lobry J.R. Properties of a general model of DNA evolution under no-strand-bias conditions. J. Mol. Evol. 40 3 (1995) 326-330
96. Lucas I., Palakodeti A., Jiang Y., Young D.J., Jiang N., Fernald A.A., and Le Beau M.M. High-throughput mapping of origins of replication in human cells. EMBO Rep. 8 8 (2007) 770-777
97. Mallat S. A Wavelet Tour in Signal Processing (1998), Academic Press, New York
98. Mallat S., and Hwang W. Singularity detection and processing with wavelets. IEEE Trans. Info. Theory 38 2 (1992) 617-643
99. Mallat S., and Zhong S. Characterization of signals from multiscale edges. IEEE Trans. Patt. Recogn. Mach. Intell. 14 7 (1992) 710-732
100. Mantegna R.N., Buldyrev S.V., Goldberger A.L., Havlin S., Peng C.-K., Simons M., and Stanley H.E. Systematic analysis of coding and noncoding DNA sequences using methods of statistical linguistics. Phys. Rev. E 52 3 (1995) 2939-2950
101. McNairn A.J., and Gilbert D.M. Epigenomic replication: Linking epigenetics to DNA replication. Bioessays 25 7 (2003) 647-656
102. Méchali M. DNA replication origins: From sequence specificity to epigenetics. Nat. Rev. Genet. 2 8 (2001) 640-645
103. In: Meyer Y. (Ed). Wavelets and Applications (1992), Springer, Berlin
104. In: Meyer Y., and Roques S. (Eds). Progress in Wavelets Analysis and Applications (1993), Éditions Frontières, Gif-sur-Yvette
105. Mordant N., Delour J., Léveque E., Arneodo A., and Pinton J.-F. Long-time correlations in Lagrangian dynamics: A key to intermittency in turbulence. Phys. Rev. Lett. 89 25 (2002) 254502
106. Mordant N., Delour J., Léveque E., Michel O., Arneodo A., and Pinton J.-F. Lagrangian velocity fluctuations in fully developed turbulence: Scaling, intermittency and dynamics. J. Stat. Phys. 113 5-6 (2003) 701-717
107. Moukhtar J., Fontaine E., Faivre-Moskalenko C., and Arneodo A. Probing persistence in DNA curvature properties with atomic force microscopy. Phys. Rev. Lett. 98 17 (2007) 178101
108. Mrázek J., and Karlin S. Strand compositional asymmetry in bacterial and large viral genomes. Proc. Natl. Acad. Sci. USA 95 7 (1998) 3720-3725
109. Muzy J.-F., Bacry E., and Arneodo A. Wavelets and multifractal formalism for singular signals: Application to turbulence data. Phys. Rev. Lett. 67 25 (1991) 3515-3518
110. Muzy J.-F., Bacry E., and Arneodo A. Multifractal formalism for fractal signals: The structure-function approach versus the wavelet-transform modulus-maxima method. Phys. Rev. E 47 2 (1993) 875-884
111. Muzy J.-F., Bacry E., and Arneodo A. The multifractal formalism revisited with wavelets. Int. J. Bifurc. Chaos 4 (1994) 245-302
112. Muzy J.-F., Sornette D., Delour J., and Arneodo A. Multifractal returns and hierarchical portfolio theory. Quant. Finance 1 (2001) 131-148
113. Nee S. Uncorrelated DNA walks. Nature 357 6378 (1992) 450
114. S. Nicolay, Analyse des séquences d'ADN par la transformée en ondelettes : extraction d'informations structurelles, dynamiques et fonctionnelles, Ph.D. thesis, University of Liège, Belgium, 2006
115. Nicolay S., Argoul F., Touchon M., d'Aubenton-Carafa Y., Thermes C., and Arneodo A. Low frequency rhythms in human DNA sequences: A key to the organization of gene location and orientation?. Phys. Rev. Lett. 93 10 (2004) 108101
116. Nicolay S., Brodie of Brodie E.-B., Touchon M., Audit B., d'Aubenton-Carafa Y., Thermes C., and Arneodo A. Bifractality of human DNA strand-asymmetry profiles results from transcription. Phys. Rev. E 75 3 (2007) 032902
117. Peng C.-K., Buldyrev S.V., Goldberger A.L., Havlin S., Sciortino F., Simons M., and Stanley H.E. Long-range correlations in nucleotide sequences. Nature 356 6365 (1992) 168-170
118. Peng C.-K., Buldyrev S.V., Goldberger A.L., Havlin S., Simons M., and Stanley H.E. Finite-size effects on long-range correlations: Implications for analysing DNA sequences. Phys. Rev. E 47 5 (1993) 3730-3733
119. Peng C.-K., Buldyrev S.V., Havlin S., Simons M., Stanley H.E., and Goldberger A.L. Mosaic organization of DNA nucleotides. Phys. Rev. E 49 2 (1994) 1685-1689
120. Rocha E.P., Danchin A., and Viari A. Universal replication biases in bacteria. Mol. Microbiol. 32 1 (1999) 11-16
121. Roux S.G., Arneodo A., and Decoster N. A wavelet-based method for multifractal image analysis. III. Applications to high-resolution satellite images of cloud structure. Eur. Phys. J. B 15 4 (2000) 765-786
122. Roux S., Muzy J.-F., and Arneodo A. Detecting vorticity filaments using wavelet analysis: About the statistical contribution of vorticity filaments to intermittency in swirling turbulent flows. Eur. Phys. J. B 8 2 (1999) 301-322
123. Roux S., Venugopal V., Fineberg K., Arneodo A., and Foufoula-Georgiou E. Evidence for inherent nonlinearity in temporal rainfall. Adv. Water Resour. 32 (2009) 41-48
124. Rudner R., Karkas J.D., and Chargaff E. Separation of B. subtilis DNA into complementary strands. 3. Direct analysis. Proc. Natl. Acad. Sci. USA 60 3 (1968) 921-922
125. In: Ruskai M., Beylkin G., Coifman R., Daubechies I., Mallat S., Meyer Y., and Raphael L. (Eds). Wavelets and Their Applications (1992), Jones and Barlett, Boston
126. Sasaki T., Sawado T., Yamaguchi M., and Shinomiya T. Specification of regions of DNA replication initiation during embryogenesis in the 65-kilobase DNApolalpha-dE2F locus of Drosophila melanogaster. Mol. Cell. Biol. 19 1 (1999) 547-555
127. Schübeler D., Scalzo D., Kooperberg C., van Steensel B., Delrow J., and Groudine M. Genome-wide DNA replication profile for Drosophila melanogaster: A link between transcription and replication timing. Nat. Genet. 32 3 (2002) 438-442
128. Shioiri C., and Takahata N. Skew of mononucleotide frequencies, relative abundance of dinucleotides and DNA strand asymmetry. J. Mol. Evol. 53 4-5 (2001) 364-376
129. In: Silverman B., and Vassilicos J. (Eds). Wavelets: The Key to Intermittent Information? (2000), Oxford University Press, Oxford
130. Stanley H.E., Buldyrev S.V., Goldberger A.L., Havlin S., Ossadnik S.M., Peng C.-K., and Simons M. Fractal landscapes in biological systems. Fractals 1 3 (1993) 283-301
131. Svejstrup J.Q. Mechanisms of transcription-coupled DNA repair. Nat. Rev. Mol. Cell Biol. 3 1 (2002) 21-29
132. The ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447 7146 (2007) 799-816
133. Tillier E.R., and Collins R.A. The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. J. Mol. Evol. 50 3 (2000) 249-257
134. Torresani B. Analyse Continue par Ondelettes (1998), Éditions de Physique, Les Ulis
135. M. Touchon, Biais de composition chez les mammifères : rôle de la transcription et de la réplication, Ph.D. thesis, University Denis Diderot, Paris VII, France, 2005
136. Touchon M., Arneodo A., d'Aubenton-Carafa Y., and Thermes C. Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes. Nucl. Acids Res. 32 17 (2004) 4969-4978
137. Touchon M., Nicolay S., Arneodo A., d'Aubenton-Carafa Y., and Thermes C. Transcription-coupled TA and GC strand asymmetries in the human genome. FEBS Lett. 555 3 (2003) 579-582
138. Touchon M., Nicolay S., Audit B., Brodie of Brodie E.-B., d'Aubenton-Carafa Y., Arneodo A., and Thermes C. Replication-associated strand asymmetries in mammalian genomes: Toward detection of replication origins. Proc. Natl. Acad. Sci. USA 102 28 (2005) 9836-9841
139. Vaillant C., Audit B., and Arneodo A. Thermodynamics of DNA loops with long-range correlated structural disorder. Phys. Rev. Lett. 95 6 (2005) 068101
140. Vaillant C., Audit B., and Arneodo A. Experiments confirm the influence of genome long-range correlations on nucleosome positioning. Phys. Rev. Lett. 99 21 (2007) 218103
141. Vaillant C., Audit B., Thermes C., and Arneodo A. Formation and positioning of nucleosomes: Effect of sequence-dependent long-range correlated structural disorder. Eur. Phys. J. E 19 3 (2006) 263-277
142. Venugopal V., Roux S.G., Foufoula-Georgiou E., and Arneodo A. Revisiting multifractality of high-resolution temporal rainfall using a wavelet-based formalism. Water Resour. Res. 42 6 (2006) W06D14
143. Venugopal V., Roux S.G., Foufoula-Georgiou E., and Arneodo A. Scaling behavior of high resolution temporal rainfall: New insights from a wavelet-based cumulant analysis. Phys. Lett. A 348 3-6 (2006) 335-345
144. Viswanathan G.M., Buldyrev S.V., Havlin S., and Stanley H.E. Long-range correlation measures for quantifying patchiness: Deviations from uniform power-law scaling in genomic DNA. Physica A 249 1-4 (1998) 581-586
145. Voss R.F. Evolution of long-range fractal correlations and 1 / f noise in DNA base sequences. Phys. Rev. Lett. 68 25 (1992) 3805-3808
146. Voss R.F. Long-range fractal correlations in DNA introns and exons. Fractals 2 1 (1994) 1-6
147. L. Zaghloul, A. Arneodo, C. Thermes, B. Audit, Large replication domains with homogeneous composition delimit heterochromatic gene deserts, in preparation