K-mer natural vector and its application to the phylogenetic analysis of genetic sequences.
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Shek-Chung Yau | Jia Wen | S. Yau | Jia Wen | Raymond H F Chan | Rong L He | Stephen S T Yau | R. Chan | Shek-Chung Yau | R. He
[1] Shek-Chung Yau,et al. Protein space: a natural method for realizing the nature of protein universe. , 2013, Journal of theoretical biology.
[2] Tiee-Jian Wu,et al. Optimal word sizes for dissimilarity measures and estimation of the degree of dissimilarity between DNA sequences , 2005, Bioinform..
[3] N. Takahata,et al. Allelic genealogy and human evolution. , 1993, Molecular biology and evolution.
[4] Se-Ran Jun,et al. Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions , 2009, Proceedings of the National Academy of Sciences.
[5] W. Atchley,et al. Molecular evolution of the MyoD family of transcription factors. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[6] Michael W. Berry,et al. An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage , 2004, BMC Bioinformatics.
[7] Se-Ran Jun,et al. Whole-genome phylogeny of mammals: Evolutionary information in genic and nongenic regions , 2009, Proceedings of the National Academy of Sciences.
[8] Richard,et al. Patterns of Divergence During Evolution of cll ,-Proteinase Inhibitors in Mammals , 1998 .
[9] Tianming Wang,et al. A novel statistical measure for sequence comparison on the basis of k-word counts. , 2013, Journal of theoretical biology.
[10] J. Bull,et al. Combining data in phylogenetic analysis. , 1996, Trends in ecology & evolution.
[11] Michael M. Miyamoto,et al. Molecular and Morphological Supertrees for Eutherian (Placental) Mammals , 2001, Science.
[12] Elizabeth R. Jessup,et al. Matrices, Vector Spaces, and Information Retrieval , 1999, SIAM Rev..
[13] Saurabh Sinha,et al. A statistical method for alignment-free comparison of regulatory sequences , 2007, ISMB/ECCB.
[14] W. Hauswirth,et al. Nucleotide sequence evidence for rapid genotypic shifts in the bovine mitochondrial DNA D-loop , 1983, Nature.
[15] S. Pääbo,et al. Mitochondrial genome variation and the origin of modern humans , 2000, Nature.
[16] M. Nei,et al. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. , 1993, Molecular biology and evolution.
[17] J. Faith,et al. Evolution of base-substitution gradients in primate mitochondrial genomes. , 2005, Genome research.
[18] D. Hillis,et al. Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis. , 1993, Molecular biology and evolution.
[19] J. Qi,et al. Whole Proteome Prokaryote Phylogeny Without Sequence Alignment: A K-String Composition Approach , 2003, Journal of Molecular Evolution.
[20] Troy Hernandez,et al. Real Time Classification of Viruses in 12 Dimensions , 2013, PloS one.
[21] A. Meyer,et al. Complete mitochondrial genome suggests diapsid affinities of turtles. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[22] S. Hedges,et al. Molecular evidence for the origin of birds. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[23] Raymond H. Chan,et al. Composition Vector Method Based on Maximum Entropy Principle for Sequence Comparison , 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[24] Xuhua Xia,et al. Rapid evolution of animal mitochondrial DNA , 2012 .
[25] Guohua Huang,et al. Alignment-free comparison of genome sequences by a new numerical characterization. , 2011, Journal of theoretical biology.
[26] J. Leunissen,et al. Protein sequences indicate that turtles branched off from the amniote tree after mammals , 1996, Journal of Molecular Evolution.
[27] Tiee-Jian Wu,et al. Statistical Measures of DNA Sequence Dissimilarity under Markov Chain Models of Base Composition , 2001, Biometrics.
[28] I. Korf,et al. Applying word-based algorithms: the IMEter. , 2009, Methods in molecular biology.
[29] Chenglong Yu,et al. A Novel Method of Characterizing Genetic Sequences: Genome Space with Biological Distance and Applications , 2011, PloS one.
[30] Xuhua Xia,et al. 18S ribosomal RNA and tetrapod phylogeny. , 2003, Systematic biology.
[31] M. Ruvolo,et al. Geographic Origins of Human Mitochondrial DNA: Phylogenetic Evidence from Control Region Sequences , 1992 .
[32] M. Nei,et al. A Simple Method for Estimating and Testing Minimum-Evolution Trees , 1992 .
[33] J. Ausió,et al. The histidine-rich protamine from ostrich and tinamou sperm. A link between reptile and bird protamines. , 1999, Biochemistry.
[34] J. Leader,et al. A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes. , 2002, Molecular biology and evolution.
[35] B. Lang,et al. Evolution of the WANCY region in amniote mitochondrial DNA. , 1994, Molecular biology and evolution.
[36] Jia Wen,et al. A 2D graphical representation of protein sequence and its numerical characterization , 2009 .
[37] Hongjie Yu. Segmented K-mer and its application on similarity analysis of mitochondrial genome sequences. , 2013, Gene.
[38] K. Chu,et al. Phylogeny of Prokaryotes and Chloroplasts Revealed by a Simple Composition Approach on All Protein Sequences from Complete Genomes Without Sequence Alignment , 2005, Journal of Molecular Evolution.
[39] S. Hedges,et al. Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequences and a review of the evidence for amniote relationships. , 1990, Molecular biology and evolution.
[40] J. A. Studier,et al. A note on the neighbor-joining algorithm of Saitou and Nei. , 1988, Molecular biology and evolution.
[41] B. Blaisdell. A measure of the similarity of sets of sequences not requiring sequence alignment. , 1986, Proceedings of the National Academy of Sciences of the United States of America.
[42] Steven A. Benner,et al. Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily , 1995, Nature.
[43] J. Klein,et al. MHC polymorphism pre-dating speciation , 1988, Nature.
[44] M. Nei,et al. Divergent evolution and evolution by the birth-and-death process in the immunoglobulin VH gene family. , 1994, Molecular biology and evolution.
[45] Se-Ran Jun,et al. Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution , 2009, Proceedings of the National Academy of Sciences.
[46] M. Nei,et al. Phylogenetic analysis in molecular evolutionary genetics. , 1996, Annual review of genetics.
[47] D. Davison,et al. A measure of DNA sequence dissimilarity based on Mahalanobis distance between frequencies of words. , 1997, Biometrics.
[48] N. Saitou,et al. The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.
[49] A. Janke,et al. The complete mitochondrial genome of Alligator mississippiensis and the separation between recent archosauria (birds and crocodiles). , 1997, Molecular biology and evolution.
[50] H Baumann,et al. Patterns of divergence during evolution of alpha 1-proteinase inhibitors in mammals. , 1996, Molecular biology and evolution.
[51] S. Karnik,et al. Angiotensin II-Forming Activity in a Reconstructed Ancestral Chymase , 1996, Science.
[52] E. Harley,et al. Housekeeping genes for phylogenetic analysis of eutherian relationships. , 2006, Molecular biology and evolution.
[53] Changchuan Yin,et al. A Novel Construction of Genome Space with Biological Geometry , 2010, DNA research : an international journal for rapid publication of reports on genes and genomes.
[54] G. Wistow,et al. Lens crystallins: gene recruitment and evolutionary dynamism. , 1993, Trends in biochemical sciences.
[55] M. Nei,et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.
[56] H. Cann,et al. Maternal inheritance of human mitochondrial DNA. , 1980, Proceedings of the National Academy of Sciences of the United States of America.