Russian version English version
About the Journal
Editorial Board
Instructions for Authors
Information for Readers and Authors
Current Issue
Archive
Contact Us
Search

Send manuscript
 


Volume 6   Issue 2   Year 2011
References

  1. Bogan JA, Natale DA, Depamphilis ML. Initiation of eukaryotic DNA replication: conservative or liberal? J. Cell. Physiol. 2000;184(2):139-150.
  2. Raghuraman MK, Winzeler EA, Collingwood D, Hunt S, Wodicka L, Conway A, Lockhart DJ, Davis RW, Brewer BJ, Fangman WL. Replication Dynamics of the Yeast Genome. Science. 2001;294(5540):115-121. doi: 10.1126/science.294.5540.115
  3. Bell SP and Dutta A. DNA replication in eukariotic cells. Annual Review of Biochemistry. 2002;71(1):333-374. doi: 10.1146/annurev.biochem.71.110601.135425
  4. Liachko I, BhaskarA, Lee C, Chung S C, Tye B-K, Keich U. A Comprehensive Genome-Wide Map of Autonomously Replicating Sequences in a Naive Genome. PLoS Genet. 2010;6(5):e1000946. doi: 10.1371/journal.pgen.1000946
  5. Gilbert DM. Making sense of eukaryotic DNA replication origins. Science. 2001;294(5540):96-100. doi: 10.1126/science.1061724
  6. Bogan JA, Natale DA, and Depamphilis ML. Initiation of eukaryotic DNA replication: conservative or liberal? Journal of Cellular Physiology. 2000;184(2):139-150. doi: 10.1002/1097-4652(200008)184:2<139::AID-JCP1>3.0.CO;2-8
  7. Demeret C, Vassetzky Y, and Mechali M. Chromatin remodelling and DNA replication: from nucleosomes to loop domains. Oncogene. 2001;20(24):3086-3093. doi: 10.1038/sj.onc.1204333
  8. Mechali M. DNA replication origins: from sequence specificity to epigenetics. Nature reviews. Genetics. 2001;2(8):640-645. doi: 10.1038/35084598
  9. McNairn AJ and Gilbert DM. Epigenomic replication: linking epigenetics to DNA replication. BioEssays : news and reviews in molecular, cellular and developmental biology. 2003;25(7):647-656. doi: 10.1002/bies.10305
  10. Bajic VB, Bajic IV, Hide W. A new method of spectral analysis of DNA/RNA and protein sequences. Plenary lecture. In: Proc. First International Conference on Bioinformatics of Genome Regulation and Structure (BGRS’98). Novosibirsk, Russia. 1998;1:120-123.
  11. Oueslati AE, Lachiri Z, Ellouze N. Spectral analysis of DNA sequence: The exon's location method. In: Proceedings of the 2007 15th International Conference on Digital Signal Processing. Sanei S et al., eds. New York: IEEE, 2007; pp. 115-118.
  12. Haimovich AD, Byrne B, Ramaswamy R, Welsh WJ. Wavelet analysis of DNA walks. Journal of Computational Biology. 2006;13(7):1289-1298. doi: 10.1089/cmb.2006.13.1289
  13. Chang CQ, Fung PC, Hung YS. Improved gene prediction by resampling-based spectral analysis of DNA sequence. In: 2008 International Special Topic Conference on Information Technology and Applications in Biomedicine. 2008; pp. 221-224. doi: 10.1109/ITAB.2008.4570626
  14. Mena-Chalco JP, Carrer H, Zana Y, Cesar RM. Identification of protein coding regions using the modified Gabor-wavelet transform. IEEE-ACM Transactions on Computational Biology and Bioinformatics. 2008;5(2):198-207. doi: 10.1109/TCBB.2007.70259
  15. Bucur A, van Leeuwen J, Dimitrova N, Mittal C. Frequency Sorting Method for Spectral Analysis of DNA Sequences. In: 2008 IEEE International Conference on Bioinformatics and Biomedicine. Los Alamitos: IEEE Computer Soc., 2008;1:43-50.
  16. Berger JA, Mitra SK, Astola J. Power spectrum analysis for DNA sequences. In: Seventh International Symposium on Signal Processing and Its Applications. New York: IEEE, 2003;2:29-32.
  17. Lobzin VV, Chechetkin VR. Order and correlations in genomic DNA sequences. The spectral approach. Phys.-Usp. 2000;43:55.
  18. Qiu JD, Sun XY, Huang JH, Liang RP. Prediction of the Types of Membrane Proteins Based on Discrete Wavelet Transform and Support Vector Machines. Protein Journal. 2010;29(2):114-119. doi: 10.1007/s10930-010-9230-z
  19. Zhang SL and Wang TM. Feature analysis of protein structure by using discrete Fourier transform and continuous wavelet transform. Journal of Mathematical Chemistry. 2009;46(2):562-568. doi: 10.1007/s10910-008-9480-6
  20. Turutina VP, Laskin AA, Kudryashov NA, Skryabin KG and Korotkov EV. Identification of latent periodicity in amino acid sequences of protein families. Biochemistry (Moscow);71(1):18-31.
  21. Karnani N, Taylor CM, Malhotra A, Dutta A. Genomic Study of Replication Initiation in Human Chromosomes Reveals the Influence of Transcription Regulation and Chromatin Structure on Origin Selection. Mol. Biol. of Cell. 2010;21(3):393-404.
  22. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The Human Genome Browser at UCSC. Genome Research. 2002;12(6):996-1006. doi: 10.1101/gr.229102. Article published online before print in May 2002
  23. Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, Zweig AS, Fujita PA, Learned K, Rhead B, Smith KE, Kuhn RM, Karolchik D, Haussler D, Kent WJ. ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Research. 2010;38(suppl 1):D620-D625. doi: 10.1093/nar/gkp961
  24. Davydov AV. Veivlety i veivletnyi analiz signalov (Wavelets and wavelet analysis of signals). 2007. Available at: http://prodav.narod.ru/wavelet/ (accessed 21 May 2011) (in Russ.).
  25. Astaf'eva NM. Wavelet analysis: basic theory and some applications. Phys.-Usp. 1996. 39: 1085. doi: 10.1070/PU1996v039n11ABEH000177
  26. Haar A. Zur Theorie der orthogonalen Funktionensysteme. Mathematische Annalen. 1910;69(3):331-371. doi: 10.1007/BF01456326
  27. Chui CK. An introduction to wavelets. San-Diego, Ca, USA: Academic Press Professional, Inc, 1992.  266 p.
  28. Abdurashidova G, Deganuto M, Klima R, Riva S, Biamonti G, Giacca M, Falaschi A. Start sites of bidirectional DNA synthesis at the human lamin B2 origin. Science. 2000;287(5460):2023-2026. doi: 10.1126/science.287.5460.2023
  29. Marchetti L, Comelli L, D'Innocenzo B, Puzzi L, Luin S, Arosio D, Calvello M, Mendoza-Maldonado R, Peverali F, Trovato F, Riva S, Biamonti G, Abdurashidova G, Beltram F, Falaschi A. Homeotic proteins participate in the function of human-DNA replication origins. Nucleic Acids Research. 2010;38(22):8105-8119. doi: 10.1093/nar/gkq688
  30. Falaschi A, Abdurashidova G, and Biamonti G. DNA replication, development and cancer: a homeotic connection? Critical Reviews in Biochemistry and Molecular Biology. 2010;45(1):14-22. doi: 10.3109/10409230903365608
  31. Del Bene F, Wittbrodt J. Cell cycle control by homeobox genes in development and disease. Seminars in Cell & Developmental Biology. 2005;16(3):449-460. doi: 10.1016/j.semcdb.2005.02.001
  32. Liò P. Wavelets in bioinformatics and computational biology: state of art and perspectives. Bioinformatics. 2003;19(1):2-9. doi: 10.1093/bioinformatics/19.1.2
  33. Brodie Of Brodie EB, Nicolay S, Touchon M, Audit B, d'Aubenton-Carafa Y, Thermes C, Arneodo A. From DNA sequence analysis to modeling replication in the human genome. Physical Review Letters. 2005;94(24):248103. doi: 10.1103/PhysRevLett.94.248103
Table of Contents
Original Article
Scherbakov A., Porozov Yu. Using wavelet-transform to detecting of origin of replication in human DNA . Ìàthematical biology and bioinformatics. 2011;6(2):147-160. doi: 10.17537/2011.6.147
(published in Russian)

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References
Supplementary data

 
  Copyright IMPB RAS © 2005-2025