[1] | Bajic V., Bajic I. and Hide W (2000) “A new method of spectral analysis of DNA/RNA and protein sequences” Centre for Engineering Research. |
[2] | Eisenberg, D., Weiss, R.M., Terwillger, T.C., (1994) “The hydrophobic moment detects periodicity in protein Hydrophobicity”. Proc. Natl. Acad. Sci. 81, 140–144. |
[3] | Galleani, L. and Garello, R. (2006) “Spectral analysis of DNA sequences by entropy minimization”, 14th European Signal Processing Conference (EUSIPCO 2006), Florence, Italy, September 4-8. |
[4] | Gan, G., Ma, C. and Wu, J. (2007) “Data clustering: theory, algorithms, and applications”, ASA-SIAM Series on Statistics and Applied Probability, USA. |
[5] | Gordon, A. (1987) “A review of hierarchical classification”, Journal of the Royal Statistical Society. Series A (General), 150(2): 119–137. |
[6] | Gordon, A. (1996) “Hierarchical classification”, In Arabie, P., Hubert, L., and Soete, G., editors, Clustering and Classification, pages 65–121. River Edge, NJ: World Scientific. |
[7] | Guntur, S. (2007) “Study of clustering algorithms for gene expressions analysis”, Thesis submitted in partial of the requirements for the degree of Master of Technology in Computer Science and Engineering, National Institute of Technology, Rourkela, India. |
[8] | Han,^{ }Y., Han,^{ }L., Yao,^{ }Y., Li, Y. and Liu, X. (2018) “Key factors in FTIR spectroscopic analysis of DNA: the sampling technique, pretreatment temperature and sample concentration”, Analytical Methods, Issue 21, 10, 2436-2443. |
[9] | Hoang, T., Yin, C., Zheng, H. Yu, C., Lucy He, R. and Yau, S. (2015) “A new method to cluster DNA sequences using Fourier power spectrum”, J Theor Biol. 7; 372: 135-45. |
[10] | Jääskinen, V., Parkkinen, V., Cheng, L., and Corander, J. (2014) “Bayesian clustering of DNA sequences using Markov chains and a stochastic partition model“, Stat Appl Genet Mol Biol., Feb; 13(1): 105-21. doi: 10.1515/sagmb-2013-0031. |
[11] | James, B., Luczak, B. and Girgis, H. (2018) “MeShClust: an intelligent tool for clustering DNA sequences” Nucleic Acids Res. 2018 Aug 21; 46(14): e83. doi: 10.1093/nar/gky315. |
[12] | Jiang, D., Tang, C. and Zhang, A. (2004) “Cluster Analysis for Gene Expression Data: A Survey”, IEEE Trans. On knowledge and data eng., VOL. 16, NO. 11, NOVEMBER, p. 1370-1386. |
[13] | Johnson, S. (1967) “Hierarchical clustering schemes”, Psychometrika”, 32(3): 241–254. |
[14] | Kruskal, J. and Landwehr, J. (1983) “Icicle plots: Better displays for hierarchical clustering”, The American Statistician, 37(2): 162–168. |
[15] | Liu, S., Wang, Z., Chen, D., Zhang, B. Tian, R., Wu, J., Zhang, Y., Xu, K., Yang, L., Cheng, C., Ma, J., Lv, L., Zheng, Y., Hu, X., Zhang, Y., Wang, X. and Li, J. (2018) “Annotation and cluster analysis of spatiotemporaland sex-related lncRNA expression in rhesus macaque brain”, Genome Research 27:1608–1620. |
[16] | Mabrouk, M. (2017) “Advanced Genomic Signal Processing Methods in DNA Mapping Schemes for Gene Prediction Using Digital Filters”, American Journal of Signal Processing 2017, 7(1): 12-24. |
[17] | Marhon, S. and Kremer, S. (2011) “Gene prediction based on DNA spectral analysis: a literature review”, J Comput Biol., Apr; 18(4): 639-76. |
[18] | McLachlan, A. and Stewart, M. (1976) “The 14-fold periodicity in alpha-tropomyosin and the interaction with Actin“, J. Mol. Biol. 103, 271–298. |
[19] | Polovinkina, A., Krylova, I., Druzhkova, P., Ivanchenkoa, M., Meyerova, I., Zaikina, A., and Zolotykha, N. (2016) “Solving Problems of Clustering and Classification of Cancer Diseases Based on DNA Methylation”, Data Pattern Recognition and Image Analysis, Vol. 26, No. 1, pp. 176–180. |
[20] | Ruiz, G., Israel, Godínez, I., Ramos, S., Ruiz, S., Pérez, H. and Morales, J. (2018) “Genomic signal processing for DNA sequence clustering” PeerJ v.6; DOI 10.7717/peerj.4264. |
[21] | Roy, M. and Barman, S. (2011) “Spectral analysis of coding and non-coding regions of a DNA sequence by Parametric and Nonparametric methods: A comparative approach”, Annals of faculty engineering Hunedoara– International Journal Of Engineering; Tome IX; Faccicule 3; pp: 57-62. |
[22] | Sibson, R. (1973) “SLINK: An optimally efficient algorithm for the single link cluster Method”, The Computer Journal, 16(1): 30–34. |
[23] | Stoffer, D., Tyler, D. and McDougall, A. (1993) “Spectral analysis for categorical time series: Scaling and the spectral envelope”; Biometrika, 80, 611–622. |
[24] | Stoffer, D. (2012) “Frequency Domain Techniques in the Analysis of DNA Sequences”, Handbook of Statistics Volume 30, 2012, Pages 261-295. |
[25] | Tavar´e, S., Giddings, B. (1989) “Some statistical aspects of the primary structure of nucleotide sequences”, In Waterman M.S. (Ed), Mathematical Methods for DNA Sequences. CRC Press, Boca Raton, Florida, pp. 117–131. |
[26] | Viari, A., Soldano, H. and Ollivier, E. (1990) “A scale-independent signal processing method for sequence analysis. Comput. Appl. Biosci. 6, 71–80. |
[27] | Ward Jr., J. (1963) “Hierarchical grouping to optimize an objective function”, Journal of the American Statistical Association, 58(301): 236–244. |
[28] | Ward Jr., J. and Hook, M. (1963) “Application of a hierarchical grouping procedure to a problem of grouping profiles”, Educational and Psychological Measurement, 23(1): 69–81. |
[29] | Waterman, M. and Vingron, M. (1994) “Sequence comparison significance and Poisson approximation”, Stat. Sci. 9, 367–381. |
[30] | Wishart, D. (1969) “256. Note: An algorithm for hierarchical classifications”, Biometrics, 25(1):165–170. |
[31] | Wu, F., Zhang, W. and Kusalik, A. (2003) “Fast genetic K-means algorithm and its application in gene expression data analysis”, BMC Bioinformatics 5(1):172, DOI: 10.1186/1471-2105-5-172. |