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| 2009 (back to top) | |
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Das, S. (2009) . Evolutionary origin and genomic organization of microRNA genes in immunoglobulin lambda variable region gene family. Mol. Biol. Evol. 26(5) 1179-1189. |
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| 2008 (back to top) | |
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Suzuki, Y. (2008) False-positive results obtained from the branch-site test of positive selection. Genes & Genetic Systems. 83:331-338. |
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| 2007 (back to top) | |
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Suzuki, Y. (2007) Inferring natural selection operating on conservative and radical substitution at single amino acid sites. Genes & Genetic Systems. 82:341-360. |
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| 2006 (back to top) | |
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Sato, A., Dongak, K., Hao, L., Takezaki, N., Shintani, S., Aoki, T., and J. Klein (2006) MHC class I genes of the cichlid fish Oreochromis niloticus. Immunogenetics 58:917- 928. |
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| 2005 (back to top) | |
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Wei, X., Hao, L., Ni, S., Liu, Q., Xu, J., and P. H. Correll (2005) Altered exon usage in the juxtamembrane domain of mouse and human RON regulates receptor activity and signaling specificity. J Biol. Chem. 280:40241-40251. |
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Klein, J. and N. Nikolaidis (2005) The descent of the antibody-based immune system by gradual evolution. Proc. Natl. Acad. Sci. USA 102:169-174. |
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Lai, Z., Wei, Shimizu, T., Ramos, E., Rohrbaugh, M., Nikolaidis, N., Ho, L., and Li, Y. (2005) Control of cell proliferation and apoptosis by mob as tumor suppressor, mats. Cell 120:675-685. |
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| 2004 (back to top) | |
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Suzuki, Y. (2004) New methods for detecting positive selection at single amino acid sites. J. Mol. Evol. 59:11-19. |
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Lee, S., J. Kim, J.-S. Son, J. Nam, D.-H. Jeong, K. Lee, S. Jang, J. Yoo, J. Lee, D.-Y. Lee, H.-G. Kang, and G. An. (2003) Systematic reverse genetic screening of T-DNA tagged genes in rice for functional genomic anaylses: MADS-box genes as a test case. Plant Cell Physiol. 44:1403-1411. |
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An, S., S. Park, D.-H. Jeong, D.-Y. Lee, H.-G. Kang, J.-H. Yu, J. Hur, S.-R. Kim, Y.-H. Kim, M. Lee, S. Han, S.-J. Kim, J. Yang, E. Kim, S. J. Wi, H. S. Chung, J.-P. Hong, V. Choe, H.-K. Lee, J.-H. Choi, J. Nam, S.-R. Kim, P.-B. Park, K. Y. Park, W. T. Kim, S. Choe, C.-B. Lee, and G. An (2003) Generation and analysis of end sequence database for T-DNA tagging lines in rice1. Plant Physiol. 133:2040-2047. |
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Hughes, A. L. and H. Piontkivska (2003) Phylogeny of trypanosomatidae and Bodonidae (Kinetoplastida) based on 18S rRNA: Evidence for paraphyly of trypanosoma and six other genera. Mol. Biol. Evol. 20:644-652. |
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Glazko, G. and H. Piontkivska (2003) Different functional categories of proteins give different estimates of divergence times for early evolution of eukaryotes. BMC Evol. Biol. (submitted) | |
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Piontkivska, H. and A. L. Hughes (2003) Evolution of vertebrate voltage-gated ion channel alfa chains by sequential gene duplication. J. Mol. Evol. 56:277-285. |
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| 2002 (back to top) | |
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Kochetov, A. V., O. A. Syrnik, I. B. Rogozin, G. V. Glazko, M. L. Komarova, and V. K. Shumnyi (2002) Context organization of mRNA 5'-untranslated regions of higher plants. Mol. Biol. (Mosk). 36:649-656. Russian. | |
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Nguyen, V. K., C. Su, S. Muyldermans, and W. van der Loo (2002) Heavy-chain antibodies in Camelidae; a case of evolutionary innovation. Immunogenetics 54:39-47. |
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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. |
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| 2000 (back to top) | |
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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. |
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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. |
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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. |
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Rooney, A. P., J. Zhang, and M. Nei (2000) An unusual form of purifying selection in a sperm protein. Mol. Biol. Evol. 17:278-283. |
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Rogozin, I. B., G. V. Glazko, and M. V. Glazkov (2000) Computer prediction of sites associated with various elements of the nuclear matrix. Brief. Bioinform. 1:33-44. |
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Rogozin, I. B., J. Lyons-Weiler, and E. V. Koonin (2000) Intron sliding in conserved gene families. Genome Analysis 16:430-432. |
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Zhang, J. (2000) Protein-length distributions for the three domains of life. Trends Genet. 16:107-109. |
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Zhang, J. (2000) Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes. J. Mol. Evol. 50:56-68. |
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| 1999 (back to top) | |
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Berikov, V. B. and I. B. Rogozin (1999) Regression trees for analysis of mutational spectra in nucleotide sequences. Bioinformatics 15:553-562. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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Zhang, J. (1999) Performance of likelihood ratio tests of evolutionary hypotheses under inadequate substitution models. Mol. Biol. Evol. 16:868-875. |
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| 1998 (back to top) | |
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Brown, J. R., J. Zhang, and J. E. Hodgson (1998) A bacterial antibiotic resistance gene with eukaryotic origins. Curr. Biol. 8:365-367. |
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Gu, X. (1998) Early metazoan divergence was about 830 million years ago. J. Mol. Evol. 47:369-371. |
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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. |
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Kumar, S. and S. B. Hedges (1998) A molecular timescale for vertebrate evolution. Nature 392:917-920. |
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Sitnikova, T. and C. Su (1998) Coevolution of immunoglobulin heavy- and light-chain variable-region gene families. Mol. Biol. Evol. 15:617-625. |
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Takezaki, N. (1998) Tie trees generated by distance methods of phylogenetic reconstruction. Mol. Biol. Evol. 15:727-737. |
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Yoshida, A., A. Rzhetsky, L. C. Hsu, and C. Chang (1998) Human aldehyde dehydrogenase gene family. Eur. J. Biochem. 251:549-557. |
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Zhang, J. and X. Gu (1998) Correlation between the substitution rate and rate variation among sites in protein evolution. Genetics 149:1615-1625. |
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| 1997 (back to top) | |
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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. |
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Gu, X. (1997) The age of the common ancestor of eukaryotes and prokaryotes: statistical inferences. Mol. Biol. Evol. 14:861-866. |
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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. |
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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. |
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Russo, C. A. M. (1997) Efficiencies of different statistical tests in supporting a known vertebrate phylogeny. Mol. Biol. Evol. 14:1078-1080. |
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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. |
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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. |
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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. |
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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. |
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Zhang, J. and S. Kumar (1997) Detection of convergent and parallel evolution at the amino acid sequence level. Mol. Biol. Evol. 14:527-536. |
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| 1996 (back to top) | |
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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. |
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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. |
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Kumar, S. (1996) A stepwise algorithm for finding minimum evolution trees. Mol. Biol. Evol. 13:584-593. |
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Kumar, S. (1996) Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates. Genetics 143:537-548. |
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Kumar, S., K. A. Balczarek, and Z.-C. Lai (1996) Evolution of the hedgehog gene family. Genetics 142:965-972. |
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Kumar, S. and A. Rzhetsky (1996) Evolutionary relationships of eukaryotic kingdoms. J. Mol. Evol. 42:183-193. |
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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. |
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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. |
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Sitnikova, T. (1996) Bootstrap method of interior-branch test for phylogenetic trees. Mol. Biol. Evol. 13:605-611. |
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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. |
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Rzhetsky, A. (1995) Estimating substitution rates in ribosomal RNA genes. Genetics 141:771-783. |
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