Geodesic
Using wavelet-transform to detecting of origin of replication in human DNA
Matematičeskaâ biologiâ i bioinformatika, Tome 6 (2011), pp. 147-160.

Voir la notice de l'article provenant de la source Math-Net.Ru

Origins of replication (ORI) prediction in human genome is very important for modern biology. The proposed approach for prediction ORI’s positions in human genome is based on finding of hidden dependencies in nucleotide sequences by the their wavelet spectra comparison. Parameters of the wavelet transform were selected on the basis of data about known ORI. Application of wavelet transform with the found parameters for the ORI prediction in sequences with unknown ORI location within random nucleotide sequences got good results. Results of the analysis of nucleotide sequences wavelet spectra can be used either alone as an indicator of ORI and as one of the factors in the different classifiers, such as the Bayesian classifier, Support Vector Machines and others. The paper listed the advantages and disadvantages of the proposed method and some possible ways to improve its effectiveness. 
@article{MBB_2011_6_a0,
     author = {A. A. Scherbakov and Yu. B. Porozov},
     title = {Using wavelet-transform to detecting of origin of replication in human {DNA}},
     journal = {Matemati\v{c}eska\^a biologi\^a i bioinformatika},
     pages = {147--160},
     publisher = {mathdoc},
     volume = {6},
     year = {2011},
     language = {ru},
     url = {http://geodesic.mathdoc.fr/item/MBB_2011_6_a0/}
}
TY  - JOUR
AU  - A. A. Scherbakov
AU  - Yu. B. Porozov
TI  - Using wavelet-transform to detecting of origin of replication in human DNA
JO  - Matematičeskaâ biologiâ i bioinformatika
PY  - 2011
SP  - 147
EP  - 160
VL  - 6
PB  - mathdoc
UR  - http://geodesic.mathdoc.fr/item/MBB_2011_6_a0/
LA  - ru
ID  - MBB_2011_6_a0
ER  - 
%0 Journal Article
%A A. A. Scherbakov
%A Yu. B. Porozov
%T Using wavelet-transform to detecting of origin of replication in human DNA
%J Matematičeskaâ biologiâ i bioinformatika
%D 2011
%P 147-160
%V 6
%I mathdoc
%U http://geodesic.mathdoc.fr/item/MBB_2011_6_a0/
%G ru
%F MBB_2011_6_a0
A. A. Scherbakov; Yu. B. Porozov. Using wavelet-transform to detecting of origin of replication in human DNA. Matematičeskaâ biologiâ i bioinformatika, Tome 6 (2011), pp. 147-160. http://geodesic.mathdoc.fr/item/MBB_2011_6_a0/

[1] 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 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/1097-4652(200008)184:2&lt;139::AID-JCP1&gt;3.0.CO;2-8'>10.1002/1097-4652(200008)184:2&lt;139::AID-JCP1&gt;3.0.CO;2-8</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=1964567'>1964567</ext-link>

[2] Raghuraman M.K., Winzeler E.A., Collingwood D., Hunt S., Wodicka L, Conway A., Lockhart D.J., Davis R.W., Brewer B.J., Fangman W.L., “Replication Dynamics of the Yeast Genome”, Science, 294:5540 (2001), 115–121 <ext-link ext-link-type='doi' href='https://doi.org/10.1126/science.294.5540.115'>10.1126/science.294.5540.115</ext-link>

[3] Bell S.P., Dutta A., “DNA replication in eukariotic cells”, Annual Review of Biochemistry, 71:1 (2002), 333–374 <ext-link ext-link-type='doi' href='https://doi.org/10.1146/annurev.biochem.71.110601.135425'>10.1146/annurev.biochem.71.110601.135425</ext-link>

[4] Liachko I., Bhaskar A., 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., 6:5 (2010), e1000946 <ext-link ext-link-type='doi' href='https://doi.org/10.1371/journal.pgen.1000946'>10.1371/journal.pgen.1000946</ext-link>

[5] Gilbert D.M., “Making sense of eukaryotic DNA replication origins”, Science, 294:5540 (2001), 96–100 <ext-link ext-link-type='doi' href='https://doi.org/10.1126/science.1061724'>10.1126/science.1061724</ext-link>

[6] Bogan J.A., Natale D.A., and Depamphilis M.L., “Initiation of eukaryotic DNA replication: conservative or liberal?”, Journal of Cellular Physiology, 184:2 (2000), 139–150 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/1097-4652(200008)184:2&lt;139::AID-JCP1&gt;3.0.CO;2-8'>10.1002/1097-4652(200008)184:2&lt;139::AID-JCP1&gt;3.0.CO;2-8</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=1964567'>1964567</ext-link>

[7] Demeret C., Vassetzky Y., and Mechali M., “Chromatin remodelling and DNA replication: from nucleosomes to loop domains”, Oncogene, 20:24 (2001), 3086–3093 <ext-link ext-link-type='doi' href='https://doi.org/10.1038/sj.onc.1204333'>10.1038/sj.onc.1204333</ext-link>

[8] Mechali M., “DNA replication origins: from sequence specificity to epigenetics”, Nature reviews. Genetics, 2:8 (2001), 640–645 <ext-link ext-link-type='doi' href='https://doi.org/10.1038/35084598'>10.1038/35084598</ext-link>

[9] McNairn A.J. and Gilbert D.M., “Epigenomic replication: linking epigenetics to DNA replication”, BioEssays : news and reviews in molecular, cellular and developmental biology, 25:7 (2003), 647–656

[10] Bajic V.B., Bajic I.V., Hide W., “A new method of spectral analysis of DNA/RNA and protein sequences”, Plenary lecture, Proc. First International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98) (Novosibirsk, Russia), v. 1, 1998, 120–123

[11] Oueslati A.E., Lachiri Z., Ellouze N., “Spectral analysis of DNA sequence: The exon's location method”, Proceedings of the 2007 15th International Conference on Digital Signal Processing, eds. S. Sanei et al., IEEE, New York, 2007, 115–118 <ext-link ext-link-type='doi' href='https://doi.org/10.1109/ICDSP.2007.4288532'>10.1109/ICDSP.2007.4288532</ext-link>

[12] Haimovich A.D., Byrne B., Ramaswamy R., Welsh W.J., “Wavelet analysis of DNA walks”, Journal of Computational Biology, 13:7 (2006), 1289–1298 <ext-link ext-link-type='doi' href='https://doi.org/10.1089/cmb.2006.13.1289'>10.1089/cmb.2006.13.1289</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=2264993'>2264993</ext-link>

[13] Chang C.Q., Fung P.C.W., Hung Y.S., “Improved gene prediction by resampling-based spectral analysis of DNA sequence”, 2008 International Special Topic Conference on Information Technology and Applications in Biomedicine, 2008, 221–224 <ext-link ext-link-type='doi' href='https://doi.org/10.1109/ITAB.2008.4570626'>10.1109/ITAB.2008.4570626</ext-link>

[14] Mena-Chalco J.P., Carrer H., Zana Y., Cesar R.M., “Identification of protein coding regions using the modified Gabor-wavelet transform”, IEEE-ACM Transactions on Computational Biology and Bioinformatics, 5:2 (2008), 198–207 <ext-link ext-link-type='doi' href='https://doi.org/10.1109/TCBB.2007.70259'>10.1109/TCBB.2007.70259</ext-link>

[15] Bucur A., van Leeuwen J., Dimitrova N., Mittal C., “Frequency Sorting Method for Spectral Analysis of DNA Sequences”, 2008 IEEE International Conference on Bioinformatics and Biomedicine, v. 1, IEEE Computer Soc, Los Alamitos, 2008, 43–50 <ext-link ext-link-type='doi' href='https://doi.org/10.1109/BIBM.2008.15'>10.1109/BIBM.2008.15</ext-link>

[16] Berger J.A., Mitra S.K., Astola J., “Power spectrum analysis for DNA sequences”, Seventh International Symposium on Signal Processing and Its Applications, v. 2, IEEE, New York, 2003, 29–32 <ext-link ext-link-type='doi' href='https://doi.org/10.1109/ISSPA.2003.1224807'>10.1109/ISSPA.2003.1224807</ext-link>

[17] Lobzin V.V., Chechetkin V.R., “Poryadok i korrelyatsii v genomnykh posledovatelnostyakh DNK. Spektralnyi podkhod”, Uspekhi fizicheskikh nauk, 170:1 (2000), 57–81

[18] Qiu J.D., Sun X.Y., Huang J.H., Liang R.P., “Prediction of the Types of Membrane Proteins Based on Discrete Wavelet Transform and Support Vector Machines”, Protein Journal, 29:2 (2010), 114–119 <ext-link ext-link-type='doi' href='https://doi.org/10.1007/s10930-010-9230-z'>10.1007/s10930-010-9230-z</ext-link>

[19] Zhang S.L. and Wang T.M., “Feature analysis of protein structure by using discrete Fourier transform and continuous wavelet transform”, Journal of Mathematical Chemistry, 46:2 (2009), 562–568 <ext-link ext-link-type='doi' href='https://doi.org/10.1007/s10910-008-9480-6'>10.1007/s10910-008-9480-6</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=2750654'>2750654</ext-link><ext-link ext-link-type='zbl-item-id' href='https://zbmath.org/?q=an:1196.92015'>1196.92015</ext-link>

[20] Turutina V.P., Laskin A.A., Kudryashov N.A., Skryabin K.G., Korotkov E.V., “Identifikatsiya skrytoi periodichnosti v aminokislotnykh posledovatelnostyakh belkovykh semeistv”, Biokhimiya, 71:1 (2006), 26–41 <ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=2251352'>2251352</ext-link>

[21] Karnani N., Taylor C.M., 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, 21:3 (2010), 393–404 <ext-link ext-link-type='doi' href='https://doi.org/10.1091/mbc.E09-08-0707'>10.1091/mbc.E09-08-0707</ext-link>

[22] Kent W.J., Sugnet C.W., Furey T.S., Roskin K.M., Pringle T.H., Zahler A.M., Haussler D., “The Human Genome Browser at UCSC”, Genome Research, 12:6 (2002), 996–1006 <ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=1902362'>1902362</ext-link>

[23] Rosenbloom K.R., Dreszer T.R., Pheasant M., Barber G.P., Meyer L.R., Pohl A., Raney B.J., Wang T., Hinrichs A.S., Zweig A.S., Fujita P.A., Learned K., Rhead B., Smith K.E., Kuhn R.M., Karolchik D., Haussler D., Kent W.J., “ENCODE whole-genome data in the UCSC Genome Browser”, Nucleic Acids Research, 38, # suppl. 1. (2010), D620–D625 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/gkp961'>10.1093/nar/gkp961</ext-link>

[24] Davydov A.V., Veivlety v veivletnyi analiz signalov, Kurs lektsii, 2007 URL: (data obrascheniya: 21.05.2011) <ext-link ext-link-type='uri' href='http://prodav.narod.ru/wavelet/'>http://prodav.narod.ru/wavelet/</ext-link>

[25] Astafeva N.M., “Veivlet-analiz: osnovy teorii i primery primeneniya”, Uspekhi fizicheskikh nauk, 166:11 (1996), 1145–1170

[26] Haar A., “Zur Theorie der orthogonalen Funktionensysteme”, Mathematische Annalen, 69:3 (1910), 331–371 <ext-link ext-link-type='doi' href='https://doi.org/10.1007/BF01456326'>10.1007/BF01456326</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=1511592'>1511592</ext-link><ext-link ext-link-type='zbl-item-id' href='https://zbmath.org/?q=an:41.0469.03'>41.0469.03</ext-link>

[27] Chui C.K., An introduction to wavelets, Academic Press Professional, Inc., San-Diego, Ca, USA, 1992, 266 pp. <ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=1150048'>1150048</ext-link>

[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, 287:5460 (2000), 2023–2026 <ext-link ext-link-type='doi' href='https://doi.org/10.1126/science.287.5460.2023'>10.1126/science.287.5460.2023</ext-link>

[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, 38:22 (2010), 8105-19 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/gkq688'>10.1093/nar/gkq688</ext-link>

[30] Falaschi A., Abdurashidova G., and Biamonti G., “DNA replication, development and cancer: a homeotic connection?”, Critical Reviews in Biochemistry and Molecular Biology, 45:1 (2010), 14–22 <ext-link ext-link-type='doi' href='https://doi.org/10.3109/10409230903365608'>10.3109/10409230903365608</ext-link>

[31] Del Bene F., Wittbrodt J., “Cell cycle control by homeobox genes in development and disease”, Seminars in Cell & Developmental Biology, 16:3 (2005), 449–460 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/j.semcdb.2005.02.001'>10.1016/j.semcdb.2005.02.001</ext-link>

[32] Liò P., “Wavelets in bioinformatics and computational biology: state of art and perspectives”, Bioinformatics, 19 (2003), 2–9 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/bioinformatics/19.1.2'>10.1093/bioinformatics/19.1.2</ext-link>

[33] Brodie Of Brodie E.B., 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, 94:24 (2005), 248103 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.94.248103'>10.1103/PhysRevLett.94.248103</ext-link>