Comparisons of classification methods for viral genomes and protein families using alignment-free vectorization

References

Baltimore, D. (1971): “Expression of animal virus genomes,” Bacteriol. Rev. 35 (3), 235–241.10.1128/br.35.3.235-241.1971Search in Google Scholar PubMed PubMed Central

Chan, R. H., R. W. Wang and H. M. Yeung (2010): “Composition vector method for phylogenetics-a review,” Proc. 9th International Symposium on Operations Research and its Applications, 13–20.Search in Google Scholar

Cortes, C. and V. Vapnik (1995): “Support-vector networks,” Machine Learning, 20, 273–297.10.1007/BF00994018Search in Google Scholar

Darling, D. A. (1975): “Note on a limit theorem,” Ann. Probab. 3, 876–878.10.1214/aop/1176996274Search in Google Scholar

Deng, M., C. Yu, Q. Liang, R. L. He, and S. S.-T. Yau (2011): “A Novel Method of Characterizing Genetic Sequences: Genome Space with Biological Distance and Applications,” PLoS One, 6 (3), e17293.10.1371/journal.pone.0017293Search in Google Scholar PubMed PubMed Central

Dudoit, S., J. Fridlyand, and T. P. Speed (2002): “Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data,” J. Am. Stat. Assoc., 97, 77–87.10.1198/016214502753479248Search in Google Scholar

Fawcett, T. (2006): “An introduction to ROC analysis,” Pattern Recognit. Lett., 27, 861–874.10.1016/j.patrec.2005.10.010Search in Google Scholar

Friedman, J. H. (1989): “Regularized discriminant analysis,” J. Am. Stat. Assoc., 84, 165–175.10.1080/01621459.1989.10478752Search in Google Scholar

Ghor, B., D. Horn, N. Goldman, Y. Levy, and T. Massingham (2009): “Genomic DNA k-mer spectra: models and modalities,” Genome Biol., 10, R108.10.1186/gb-2009-10-10-r108Search in Google Scholar

Hand, D. J. and R. J. Till (2001): “A simple generalisation of the area under the ROC curve for multiple class classification problems,” Mach. Learn., 45: 171.10.1023/A:1010920819831Search in Google Scholar

Hastie, T., R. Tibshirani, and J. Friedman (2009): The Elements of Statistical Learning: Data Mining, Inference, and Prediction, Second Edition, Springer, New York.10.1007/978-0-387-84858-7Search in Google Scholar

Hernandez, T. and J. Yang (2013): “Descriptive statistics of the genome: phylogenetic classification of viruses,” J. Comput. Biol., 23, 810–820.10.1089/cmb.2013.0132Search in Google Scholar PubMed

Hoang, T., C. Yin, H. Zheng, C. Yu, L. R. He, and S. S.-T. Yau (2015): “A new method to cluster DNA sequences using Fourier power spectrum,” J. Theor. Biol., 372, 135–145.10.1016/j.jtbi.2015.02.026Search in Google Scholar

Huang, G. H., H. Q. Zhou, Y. F. Li, and L. X. Xu (2011): “Alignment-free comparison of genome sequences by a new numerical characterization,” J. Theor. Biol., 281, 107–112.10.1016/j.jtbi.2011.04.003Search in Google Scholar

Huang, G. H. (2014): “A novel neighborhood model to predict protein function from protein-protein interaction data,” Current Bioinformatics,” 11, 237–244.10.2174/157016461104150121113959Search in Google Scholar

Huang, H.-H., T. Xu, and J. Yang (2014a): “Comparing logistic regression, support vector machines, and permanental classification methods in predicting hypertension,” BMC Proceedings, 8 (Suppl 1), S96.10.1186/1753-6561-8-S1-S96Search in Google Scholar

Huang, H.-H., C. Yu, H. Zheng, T. Hernandez, S.-C. Yau, R. L. He, J. Yang, S. S.-T. Yau (2014b): “Global comparison of multiple-segmented viruses in 12-dimensional genome space,” Mol. Phylogenet. Evol., 81, 29–36.10.1016/j.ympev.2014.08.003Search in Google Scholar

Huang, H.-H. (2016): “An ensemble distance measure of k-mer and Natural Vector for the phylogenetic analysis of multiple-segmented viruses,” J. Theor. Biol., 398, 136–144.10.1016/j.jtbi.2016.03.004Search in Google Scholar

Huang, G. H., C. Chu, T. Huang, X. Kong, Y. Zhang, N. Zhang, and Y.-D. Cai (2016): “Exploring mouse protein function via multiple approaches,” PLoS One, 11, e0166580.10.1371/journal.pone.0166580Search in Google Scholar

Huang, H.-H. and S.-B. Girimurugan (2018): “A novel real-time genome comparison method using discrete wavelet transform,” J. Comput. Biol., 25, 405–416.10.1089/cmb.2017.0115Search in Google Scholar

Maddouri, M. and M. Elloumi (2002): “A data mining approach based on machine learning techniques to classify biological sequences,” Knowl. Based Syst., 15, 2002.10.1016/S0950-7051(01)00143-5Search in Google Scholar

National Center for Biotechnology Information (NCBI)[Internet]. (2016): Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; Available from: https://www.ncbi.nlm.nih.gov/.Search in Google Scholar

Polychronopoulos, D., E. Weitschek, S. Dimitrieva, P. Bucher, G. Felici, and Y. Almirantis (2014): “Classification of selectively constrained DNA elements using feature vectors and rule-based classifiers,” Genomics 104, 79–86.10.1016/j.ygeno.2014.07.004Search in Google Scholar PubMed

Rao, C. R. and S. K. Mitra (1972): “Generalized inverse of a matrix and its applications,” Proc. Sixth Berkeley Symp. on Math. Statist. and Prob., Vol. 1, Univ. of Calif. Press, 601–620.10.1525/9780520325883-032Search in Google Scholar

Selcuk, K., G. Dincer, and Z. Gokmen (2016): MVN: an R package for assessing multivariate normality. R package vignettes.Search in Google Scholar

Sims, G. E., S. R. Jun, G. A. Wu, and S. H. Kim (2009): “Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions,” Proc. Natl. Acad. Sci. U.S.A. 106, 2677–2682.10.1073/pnas.0813249106Search in Google Scholar PubMed PubMed Central

Vinga, S. and J. Almeida (2003): “Alignment-free sequence comparison review.” Bioinformatics, 19, 513–523.10.1093/bioinformatics/btg005Search in Google Scholar PubMed

Vinga, S. (2007): Biological sequence analysis by vector-valued functions: revisiting alignment-free methodologies for DNA and protein classification. In: Pham, T. D., Yan, H., Crane, D. I. (Eds.), Advanced Computational Methods for Biocomputing and Bioimaging. Nova Science Publishers, New York.Search in Google Scholar

Weitschek, E., F. Cunial and G. Felici (2015): “LAF: logic alignment free and its application to bacterial genomes classification,” BioData Min., 8, 39.10.1186/s13040-015-0073-1Search in Google Scholar PubMed PubMed Central

Yu, C., T. Hernandez, H. Zheng, S.-C. Yau, H.-H. Huang, R. L. He, J. Yang, and S. S.-T. Yau (2013): “Real time classification of viruses in 12 dimensions,” PLoS One, 8, e64328.10.1371/journal.pone.0064328Search in Google Scholar PubMed PubMed Central