[1] Zhurkin, V.B. (1983) Specific alignment of nucleosomes on DNA correlates with periodic distribution of purine- pyrimidine and pyrimidine-purine dimers. FEBS Letters, 158(2), 293-297.
[2] Sarchwell, S.C., Drew, H.R. and Travers, A.A. (1986) Sequence periodicities in chicken nucleosome core DNA. Journal of Molecular Biology, 191(4), 659-675.
[3] Simpson, R.T. (1991) Nucleosome positioning: Occu- rrence, mechanisms, and functional consequences. Pro- gress in Nucleic Acid Research and Molecular Biology, 40, 143-184.
[4] Peckham, H.E., Thurman, R.E., Fu, Y., Stamato- yannopoulos, J.A., Nobel, W.S., Struhl, K. and Weng, Z. (2007) Nucleosome positioning signals in genomic DNA. Genome Research, 17(8), 1170-1177.
[5] Salih, F., Salih, B. and Trifonov, E.N. (2008) Sequence structure of hidden 10.4-base repeat in the nucleosomes of C. elegans. Journal of Biomolecular Structure and Dynamics, 26(3), 273-281.
[6] Trifonov, E.N. (1998) 3-, 10.5-, 200- and 400-base perio- dicities in genome sequences. Physica A, 249(1-4), 511- 516.
[7] Widom, J. (2001) Role of DNA sequence in nucleosome stability and dynamics. Quarterly Reviews of Biophysics, 34, 269-324.
[8] Segal, E., Fondufe-Mittendorf, Y., Chen, L., Thåström, A., Field, Y., Moore, I.K., Wang, J.Z. and Widom, J. (2006) A genomic code for nucleosome positioning. Nature, 442(7104), 772-778.
[9] Tolstorukov, M.Y., Colasanti, A.V., McCandlish, D.M., Olson, W.K. and Zhurkin, V.B. (2007) A novel roll-and- slide mechanism of DNA folding in chromatin: Impli- cations for nucleosome positioning. Journal of Molecular Biology, 371(3), 725-738.
[10] Bolshoy, A., McNamara, P., Harrington, R.E. and Trifonov, E.N. (1991) Curved DNA without A-A: Experimental estimation of all 16 DNA wedge angles. Proceedings of the National Academy of Sciences, 88(6), 2312-2316.
[11] Packer, M.J., Dauncey, M.P. and Hunter, C.A. (2000) Sequence-dependent DNA structure: Dinucleotide confor mational maps. Journal of Molecular Biology, 295(1), 71-83.
[12] Bishop, T.C. (2005) Molecular dynamics simulations of a nucleosome and free DNA. Journal of Biomolecular Structure and Dynamics, 22(6), 673-686.
[13] Fujii, S., Kono, H., Takenaka, S., Go, N. and Sarai, A. (2007) Sequence-dependent DNA deformability studied using molecular dynamics simulations. Nucleic Acids Research, 35(18), 6063-6074.
[14] Olson, W.K., Gorin, A.A., Lu, X., Hock, L.M. and Zhurkin, V.B. (1998) DNA sequence-dependent defor- mability deduced from protein-DNA crystal complexes. Proceedings of the National Academy of Sciences, 95(19), 11163-11168.
[15] Lu, X. and Olson, W.K. (2003) 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Research, 31(17), 5108-5121.
[16] Trifonov, E.N. (1980) Sequence-dependent deforma- tional anisotropy of chromatin DNA. Nucleic Acids Research, 8(17), 4041-4053.
[17] Worning, P., Jensen, L.J., Nelson, K.E., Brunak, S. and Ussery, D.W. (2000) Structural analysis of DNA se- quence: Evidence for lateral gene transfer in Thermotoga maritima. Nucleic Acids Research, 28(3), 706-709.
[18] Liu, H., Wu, J., Xie, J., Yang, X., Lu, Z. and Sun, X. (2008) Characteristics of nucleosome core DNA and their applications in predicting nucleosome positions. Biophy- sical Journal, 94(12), 4597-4604.
[19] Wu, Q., Wang J. and Yan, H. (2009) Prediction of nucleosome positions in the yeast genome based on matched mirror position filtering. Bioinformation, 3(10), 454-459.
[20] Suzuki, M., Yagi, N. and Finch, J.T. (1996) Role of base-backbone and base-base interactions in alternating DNA conformations. FEBS letters, 379(2), 148-152.
[21] Suzuki, M., Amano, N., Kakinuma, J. and Tateno, M. (1997) Use of a 3D structure data base for understanding sequence-dependent conformational aspects of DNA. Journal of Molecular Biology, 274(3), 421-435.
[22] Sarai, A., Mazur, J., Nussinov, R. and Jernigan, R.L. (1989) Sequence dependence of DNA conformational flexibility. Biochemistry, 28(19), 7842-7849.
[23] Young, M.A., Ravishanker, G., Beveridge, D.L. and Berman, H.M. (1995) Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA- protein complexes. Biophysical Journal, 68(6), 2454- 2468.
[24] Bharanidharan, D. and Gautham, N. (2006) Principle component analysis of DNA oligonucleotide structural data. Biochemical and Biophysical Research Commu- nications, 340(4), 1229-1237.