IMEG - Publications

2001 (back to top)
	Glazko, G. V., I. B. Rogozin, and M. V. Glazkov (2001) Comparative study and prediction of DNA fragments associated with various elements of the nuclear matrix. Biochim. Biophys. Acta 1517:351-364.

	Nguyen, V. K., C. Su, and S. Muyldermans (2001) Heavy-chain antibodies in Camelidae; a case of evolutionary innovation. Immunogenetics 54:39-47.

2000 (back to top)
	Mayorov, V. I., I. B. Rogozin, E. A. Elisaphenko, and L. R. Adkison (2000) B2 elements present in the human genome. Mamm. Genome 11:177-179.

	Morozov, P., T. Sitnikova, G. Churchill, F. J. Ayala, and A. Rzhetsky (2000) A new method for characterizing replacement rate variation in molecular sequences: application of the fourier and wavelet models to drosophila and mammalian proteins. Genetics 154:381-395.

	Ota, T., T. Sitnikova, and M. Nei (2000) Evolution of vertebrate immunoglobulin variable gene segments. Curr. Top. Microbiol. Immunol. 248:221-245.

	Purdom Jr, P. W., P. G. Bradford, K. Tamura, and S. Kumar (2000) Single column discrepancy and dynamic max-mini optimizations for quickly finding the most parsimonious evolutionary trees. Bioinformatics 16:140-151.

	Rogozin, I. B., G. V. Glazko, and M. V. Glazkov (2000) Computer prediction of sites associated with various elements of the nuclear matrix. Bioinformatics 1:33-44.

	Rogozin, I. B., J. Lyons-Weiler, and E. V. Koonin (2000) Intron sliding in conserved gene families. Genome Analysis 16:430-432.

	Zhang, J. (2000) Protein-length distributions for the three domains of life. Trends Genet. 16:107-109.

	Zhang, J. (2000) Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes. J. Mol. Evol. 50:56-68.

1999 (back to top)
	Berikov, V. B. and I. B. Rogozin (1999) Regression trees for analysis of mutational spectra in nucleotide sequences. Bioinformatics 15:553-562.

	Lyons-Weiler, J. and G. A. Hoelzer (1999) Null model selection, compositional bias, character state bias, and the limits of phylogenetic information. Mol. Biol. Evol. 16:1400-1405.

	Lyons-Weiler, J. and K. Takahashi (1999) Branch length heterogeneity leads to nonindependent branch length estimates and can decrease the efficiency of methods of phylogenetic inference. J. Mol. Evol. 49:392-405.

	Mayorov, V. I., I. B. Rogozin, and L. R. Adkison (1999) Characterization of several LINE-1 elements in Microtus kirgisorum. Mamm. Genome 10:724-729.

	Mayorov, V. I., I. B. Rogozin, E. A. Elisaphenko, and L. R. Adkison (1999) B2 elements present in the human genome. Mamm. Genome 11:177-179.

	Nikaido, M., A. P. Rooney, and N. Okada (1999) Phylogenetic relationships among cetartiodactyls based on insertions of short and long interspersed elements: Hippopotamuses are the closest extant relatives of whales. Proc. Natl. Acad. Sci. USA 96:10261-10266.

	Rooney, A. P., R. L. Honeycutt, S. K. Davis, and J. N. Derr (1999) Evaluating a putative bottleneck in a population of bowhead whales form patterns of microsatellite diversity and genetic disequilibria. J. Mol. Evol. 49:682-690.

	Rooney, A. P. and J. Zhang (1999) Rapid evolution of a primate sperm protein: relaxation of functional constraint or positive Darwinian selection? Mol. Biol. Evol. 16:706-710.

	Wang, D. Y.-C., S. Kumar, and S. B. Hedges (1999) Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi. Proc. R. Soc. Lond. B. 266:163-171.

	Zhang, J. (1999) Performance of likelihood ratio tests of evolutionary hypotheses under inadequate substitution models. Mol. Biol. Evol. 16:868-875.

1998 (back to top)
	Brown, J. R., J. Zhang, and J. E. Hodgson (1998) A bacterial antibiotic resistance gene with eukaryotic origins. Curr. Biol. 8:365-367.

	Gu, X. (1998) Early metazoan divergence was about 830 million years ago. J. Mol. Evol. 47:369-371.

	Gu, X. and W.-H. Li (1998) A general additive distance with time-reversibility and rate variation among nucleotide sites. Proc. Natl. Acad. Sci. USA 93:4671-4676.

	Gu, X. and W.-H. Li (1998) Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution. Proc. Natl. Acad. Sci. USA 95:5899-5905.

	Kumar, S. and S. B. Hedges (1998) A molecular timescale for vertebrate evolution. Nature 392:917-920.

	Sitnikova, T. and C. Su (1998) Coevolution of immunoglobulin heavy- and light-chain variable-region gene families. Mol. Biol. Evol. 15:617-625.

	Takezaki, N. (1998) Tie trees generated by distance methods of phylogenetic reconstruction. Mol. Biol. Evol. 15:727-737.

	Yoshida, A., A. Rzhetsky, L. C. Hsu, and C. Chang (1998) Human aldehyde dehydrogenase gene family. Eur. J. Biochem. 251:549-557.

	Zhang, J. and X. Gu (1998) Correlation between the substitution rate and rate variation among sites in protein evolution. Genetics 149:1615-1625.

1997 (back to top)
	Balczarek, K. A., Z.-C. Lai, and S. Kumar (1997) Evolution and functional diversification of the paired box (Pax) DNA-binding domains. Mol. Biol. Evol. 14:829-842.

	Gu, X. (1997) The age of the common ancestor of eukaryotes and prokaryotes: statistical inferences. Mol. Biol. Evol. 14:861-866.

	Gu, X. and J. Zhang (1997) A simple method for estimating the parameter of substitution rate variation among sites. Mol. Biol. Evol. 14:1106-1113.

	Leitner, T., S. Kumar, and J. Albert (1997) Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history. J. Virol. 71:4761-4770.

	Russo, C. A. M. (1997) Efficiencies of different statistical tests in supporting a known vertebrate phylogeny. Mol. Biol. Evol. 14:1078-1080.

	Rzhetsky, A., F. J. Ayala, L. C. Hsu, C. Chang, and A. Yoshida (1997) Exon/intron structure of aldehyde dehydrogenase genes supports the "introns-late" theory. Proc. Natl. Acad. Sci USA 94:6820-6825.

	Rzhetsky, A., F. J. Ayala, L. C. Hsu, C. Chang, and A. Yoshida (1997) Fitting models of intron evolution to aldehyde dehydrogenase data. In: Mathematical hierarchies and biology DIMACS series in discrete mathematics and theoretical computer science (B. Mirkin, F. McMorris, F. Roberts, and A. Rzhetsky, eds.) AMS, Providence, pp. 95-110.

	Taberner, A., J. Dopazo, and P. Castanera. (1997) Genetic characterization of populations of a De Novo arisen sugar beet pest, Aubeonymus mariaefranciscae (Coleptera, curculionidae), by RAPD analysis. J. Mol. Evol. 45:24-31.

	Yeager, M. S., Kumar, and A. L. Hughes (1997) Sequence convergence in the peptide-binding region of primate and rodent MHC class Ib molecules. Mol. Biol. Evol. 14:1035-1041.

	Zhang, J. and S. Kumar (1997) Detection of convergent and parallel evolution at the amino acid sequence level. Mol. Biol. Evol. 14:527-536.

1996 (back to top)
	Hedges, S. B., P. H. Parker, C. G. Sibley, and S. Kumar (1996) Continental breakup and the ordinal diversification of birds and mammals. Nature 381:226-229.

	Kumar, S. (1996) A stepwise algorithm for finding minimum evolution trees. Mol. Biol. Evol. 13:584-593.

	Kumar, S. (1996) Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates. Genetics 143:537-548.

	Kumar, S., K. A. Balczarek, and Z.-C. Lai (1996) Evolution of the hedgehog gene family. Genetics 142:965-972.

	Kumar, S. and A. Rzhetsky (1996) Evolutionary relationships of eukaryotic kingdoms. J. Mol. Evol. 42:183-193.

	Rzhetsky, A., J. Dopazo, E. Snyder, C. A. Dangler, and F. J. Ayala (1996) Assessing dissimilarity of genes by comparing their RNAse a mismatch cleavage patterns. Genetics 144:1975-1983.

	Rzhetsky, A. and T. Sitnikova (1996) When is it safe to use an oversimplified substitution model in tree-making? Mol. Biol. Evol. 13:1255-1265.

	Sitnikova, T. (1996) Bootstrap method of interior-branch test for phylogenetic trees. Mol. Biol. Evol. 13:605-611.

	Yang, Z. and S. Kumar (1996) Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites. Mol. Biol. Evol. 13:650-659. (back to top)