TY - JOUR AU - Thomson, J. M. AU - Gaucher, E. A. AU - Burgan, M. F. AU - De Kee, D. W. AU - Li, T. AU - Aris, J. P. AU - Benner, S. A. PY - 2005 DA - 2005// TI - Resurrecting ancestral alcohol dehydrogenases from yeast JO - Nat Genet VL - 37 UR - https://doi.org/10.1038/ng1553 DO - 10.1038/ng1553 ID - Thomson2005 ER - TY - JOUR AU - Gaucher, E. A. AU - Graddy, L. G. AU - Li, T. AU - Simmen, R. C. AU - Simmen, F. A. AU - Schreiber, D. R. AU - Liberles, D. A. AU - Janis, C. M. AU - Benner, S. A. PY - 2004 DA - 2004// TI - The planetary biology of cytochrome P450 aromatases JO - BMC Biol VL - 2 UR - https://doi.org/10.1186/1741-7007-2-19 DO - 10.1186/1741-7007-2-19 ID - Gaucher2004 ER - TY - JOUR AU - Kumar, S. AU - Gadagkar, S. R. PY - 2001 DA - 2001// TI - Disparity index: a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences JO - Genetics VL - 158 ID - Kumar2001 ER - TY - JOUR AU - Li, W. H. AU - Wu, C. I. AU - Luo, C. C. PY - 1985 DA - 1985// TI - A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes JO - Mol Biol Evol VL - 2 ID - Li1985 ER - TY - JOUR AU - Nei, M. AU - Gojobori, T. PY - 1986 DA - 1986// TI - Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions JO - Mol Biol Evol VL - 3 ID - Nei1986 ER - TY - JOUR AU - Yang, Z. AU - Nielsen, R. PY - 2000 DA - 2000// TI - Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026236 DO - 10.1093/oxfordjournals.molbev.a026236 ID - Yang2000 ER - TY - JOUR AU - Li, W. H. AU - Ellsworth, D. L. AU - Krushkal, J. AU - Chang, B. H. AU - Hewett-Emmett, D. PY - 1996 DA - 1996// TI - Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis JO - Mol Phylogenet Evol VL - 5 UR - https://doi.org/10.1006/mpev.1996.0012 DO - 10.1006/mpev.1996.0012 ID - Li1996 ER - TY - JOUR AU - Li, W. H. AU - Yi, S. AU - Makova, K. PY - 2002 DA - 2002// TI - Male-driven evolution JO - Curr Opin Genet Dev VL - 12 UR - https://doi.org/10.1016/S0959-437X(02)00354-4 DO - 10.1016/S0959-437X(02)00354-4 ID - Li2002 ER - TY - JOUR AU - Li, W. H. PY - 1977 DA - 1977// TI - Distribution of nucleotide differences between two randomly chosen cistrons in a finite population JO - Genetics VL - 85 ID - Li1977 ER - TY - JOUR AU - Smith, N. G. AU - Hurst, L. D. PY - 1999 DA - 1999// TI - The causes of synonymous rate variation in the rodent genome. Can substitution rates be used to estimate the sex bias in mutation rate? JO - Genetics VL - 152 ID - Smith1999 ER - TY - JOUR AU - Kumar, S. AU - Subramanian, S. PY - 2002 DA - 2002// TI - Mutation rates in mammalian genomes JO - Proc Natl Acad Sci U S A VL - 99 UR - https://doi.org/10.1073/pnas.022629899 DO - 10.1073/pnas.022629899 ID - Kumar2002 ER - TY - JOUR AU - Nachman, M. W. AU - Crowell, S. L. PY - 2000 DA - 2000// TI - Estimate of the mutation rate per nucleotide in humans JO - Genetics VL - 156 ID - Nachman2000 ER - TY - JOUR AU - Smith, N. G. AU - Webster, M. T. AU - Ellegren, H. PY - 2002 DA - 2002// TI - Deterministic mutation rate variation in the human genome JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.220502 DO - 10.1101/gr.220502 ID - Smith2002 ER - TY - JOUR AU - Yi, S. AU - Ellsworth, D. L. AU - Li, W. H. PY - 2002 DA - 2002// TI - Slow molecular clocks in Old World monkeys, apes, and humans JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004043 DO - 10.1093/oxfordjournals.molbev.a004043 ID - Yi2002 ER - TY - JOUR AU - Belle, E. M. AU - Duret, L. AU - Galtier, N. AU - Eyre-Walker, A. PY - 2004 DA - 2004// TI - The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny JO - J Mol Evol VL - 58 UR - https://doi.org/10.1007/s00239-004-2587-x DO - 10.1007/s00239-004-2587-x ID - Belle2004 ER - TY - JOUR AU - Duret, L. AU - Semon, M. AU - Piganeau, G. AU - Mouchiroud, D. AU - Galtier, N. PY - 2002 DA - 2002// TI - Vanishing GC-rich isochores in mammalian genomes JO - Genetics VL - 162 ID - Duret2002 ER - TY - JOUR AU - Hardison, R. C. AU - Roskin, K. M. AU - Yang, S. AU - Diekhans, M. AU - Kent, W. J. AU - Weber, R. AU - Elnitski, L. AU - Li, J. AU - O'Connor, M. AU - Kolbe, D. AU - Schwartz, S. AU - Furey, T. S. AU - Whelan, S. AU - Goldman, N. AU - Smit, A. AU - Miller, W. AU - Chiaromonte, F. AU - Haussler, D. PY - 2003 DA - 2003// TI - Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.844103 DO - 10.1101/gr.844103 ID - Hardison2003 ER - TY - JOUR AU - Castresana, J. PY - 2002 DA - 2002// TI - Genes on human chromosome 19 show extreme divergence from the mouse orthologs and a high GC content JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.8.1751 DO - 10.1093/nar/30.8.1751 ID - Castresana2002 ER - TY - JOUR AU - Matassi, G. AU - Sharp, P. M. AU - Gautier, C. PY - 1999 DA - 1999// TI - Chromosomal location effects on gene sequence evolution in mammals JO - Curr Biol VL - 9 UR - https://doi.org/10.1016/S0960-9822(99)80361-3 DO - 10.1016/S0960-9822(99)80361-3 ID - Matassi1999 ER - TY - JOUR AU - Malcom, C. M. AU - Wyckoff, G. J. AU - Lahn, B. T. PY - 2003 DA - 2003// TI - Genic mutation rates in mammals: local similarity, chromosomal heterogeneity, and X-versus-autosome disparity JO - Mol Biol Evol VL - 20 UR - https://doi.org/10.1093/molbev/msg178 DO - 10.1093/molbev/msg178 ID - Malcom2003 ER - TY - JOUR AU - Lercher, M. J. AU - Williams, E. J. AU - Hurst, L. D. PY - 2001 DA - 2001// TI - Local similarity in evolutionary rates extends over whole chromosomes in human-rodent and mouse-rat comparisons: implications for understanding the mechanistic basis of the male mutation bias JO - Mol Biol Evol VL - 18 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003744 DO - 10.1093/oxfordjournals.molbev.a003744 ID - Lercher2001 ER - TY - JOUR AU - Williams, E. J. AU - Hurst, L. D. PY - 2000 DA - 2000// TI - The proteins of linked genes evolve at similar rates JO - Nature VL - 407 UR - https://doi.org/10.1038/35038066 DO - 10.1038/35038066 ID - Williams2000 ER - TY - JOUR AU - Casane, D. AU - Boissinot, S. AU - Chang, B. H. AU - Shimmin, L. C. AU - Li, W. PY - 1997 DA - 1997// TI - Mutation pattern variation among regions of the primate genome JO - J Mol Evol VL - 45 UR - https://doi.org/10.1007/PL00006223 DO - 10.1007/PL00006223 ID - Casane1997 ER - TY - JOUR AU - Lercher, M. J. AU - Chamary, J. V. AU - Hurst, L. D. PY - 2004 DA - 2004// TI - Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.1597404 DO - 10.1101/gr.1597404 ID - Lercher2004 ER - TY - JOUR AU - Benner, S. A. AU - Chamberlin, S. G. AU - Liberles, D. A. AU - Govindarajan, S. AU - Knecht, L. PY - 2000 DA - 2000// TI - Functional inferences from reconstructed evolutionary biology involving rectified databases--an evolutionarily grounded approach to functional genomics JO - Res Microbiol VL - 151 UR - https://doi.org/10.1016/S0923-2508(00)00123-6 DO - 10.1016/S0923-2508(00)00123-6 ID - Benner2000 ER - TY - JOUR AU - Gaucher, E. A. AU - Miyamoto, M. M. AU - Benner, S. A. PY - 2003 DA - 2003// TI - Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein JO - Genetics VL - 163 ID - Gaucher2003 ER - TY - JOUR AU - Gaucher, E. A. AU - Gu, X. AU - Miyamoto, M. M. AU - Benner, S. A. PY - 2002 DA - 2002// TI - Predicting functional divergence in protein evolution by site-specific rate shifts JO - Trends Biochem Sci VL - 27 UR - https://doi.org/10.1016/S0968-0004(02)02094-7 DO - 10.1016/S0968-0004(02)02094-7 ID - Gaucher2002 ER - TY - JOUR AU - Eigen, M. AU - Johnson, J. S. PY - 1960 DA - 1960// TI - Kinetics of reactions in solution JO - Ann Rev Phys Chem VL - 11 UR - https://doi.org/10.1146/annurev.pc.11.100160.001515 DO - 10.1146/annurev.pc.11.100160.001515 ID - Eigen1960 ER - TY - JOUR AU - Sonnhammer, E. L. AU - Koonin, E. V. PY - 2002 DA - 2002// TI - Orthology, paralogy and proposed classification for paralog subtypes JO - Trends Genet VL - 18 UR - https://doi.org/10.1016/S0168-9525(02)02793-2 DO - 10.1016/S0168-9525(02)02793-2 ID - Sonnhammer2002 ER - TY - JOUR AU - Springer, M. S. AU - Murphy, W. J. AU - Eizirik, E. AU - O'Brien, S. J. PY - 2003 DA - 2003// TI - Placental mammal diversification and the Cretaceous-Tertiary boundary JO - Proc Natl Acad Sci U S A VL - 100 UR - https://doi.org/10.1073/pnas.0334222100 DO - 10.1073/pnas.0334222100 ID - Springer2003 ER - TY - JOUR AU - Yang, Z. PY - 1997 DA - 1997// TI - PAML: a program package for phylogenetic analysis by maximum likelihood JO - Comput Appl Biosci VL - 13 ID - Yang1997 ER - TY - JOUR AU - Lynch, M. AU - Conery, J. S. PY - 2000 DA - 2000// TI - The evolutionary fate and consequences of duplicate genes JO - Science VL - 290 UR - https://doi.org/10.1126/science.290.5494.1151 DO - 10.1126/science.290.5494.1151 ID - Lynch2000 ER - TY - JOUR AU - Yoder, A. D. AU - Yang, Z. PY - 2000 DA - 2000// TI - Estimation of primate speciation dates using local molecular clocks JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026389 DO - 10.1093/oxfordjournals.molbev.a026389 ID - Yoder2000 ER - TY - JOUR AU - Blanc, G. AU - Hokamp, K. AU - Wolfe, K. H. PY - 2003 DA - 2003// TI - A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.751803 DO - 10.1101/gr.751803 ID - Blanc2003 ER - TY - JOUR AU - Pauling, L. AU - Zuckerkandl, E. PY - 1963 DA - 1963// TI - Molecular paleontology JO - Acta Chem Scand VL - 17 (Suppl. 1) UR - https://doi.org/10.3891/acta.chem.scand.17s-0009 DO - 10.3891/acta.chem.scand.17s-0009 ID - Pauling1963 ER - TY - JOUR AU - Wilson, A. C. AU - Carson, S. S. AU - White, T. J. PY - 1977 DA - 1977// TI - The molecular clock. JO - Ann Rev Biochem VL - 46 UR - https://doi.org/10.1146/annurev.bi.46.070177.003041 DO - 10.1146/annurev.bi.46.070177.003041 ID - Wilson1977 ER - TY - JOUR AU - Ayala, F. J. PY - 1999 DA - 1999// TI - Molecular clock mirages JO - Bioessays VL - 21 UR - https://doi.org/3.0.CO;2-B DO - 3.0.CO;2-B ID - Ayala1999 ER - TY - CHAP AU - Kimura, M. T. PY - 1983 DA - 1983// BT - The Neutral Theory of Molecular Evolution PB - Cambridge CY - Cambridge Univ. Press UR - https://doi.org/10.1017/CBO9780511623486 DO - 10.1017/CBO9780511623486 ID - Kimura1983 ER - TY - JOUR AU - Pollock, D. D. PY - 1998 DA - 1998// TI - Increased accuracy in analytical molecular distance estimation JO - Theor Popul Biol VL - 54 UR - https://doi.org/10.1006/tpbi.1998.1362 DO - 10.1006/tpbi.1998.1362 ID - Pollock1998 ER - TY - JOUR AU - Hurst, L. D. PY - 2002 DA - 2002// TI - The Ka/Ks ratio: diagnosing the form of sequence evolution JO - Trends Genet VL - 18 UR - https://doi.org/10.1016/S0168-9525(02)02722-1 DO - 10.1016/S0168-9525(02)02722-1 ID - Hurst2002 ER - TY - CHAP AU - Roth, C. AU - Betts, M. J. AU - Steffansson, P. AU - Saelensminde, G. AU - Liberles, D. A. PY - 2005 DA - 2005// TI - The Adaptive Evolution Database (TAED): A phylogeny-based tool for comparative genomics BT - Nucleic Acids Research (in press) ID - Roth2005 ER - TY - JOUR AU - Messier, W. AU - Stewart, C. B. PY - 1997 DA - 1997// TI - Episodic adaptive evolution of primate lysozymes JO - Nature VL - 385 UR - https://doi.org/10.1038/385151a0 DO - 10.1038/385151a0 ID - Messier1997 ER - TY - JOUR AU - Trabesinger-Ruef, N. AU - Jermann, T. AU - Zankel, T. AU - Durrant, B. AU - Frank, G. AU - Benner, S. A. PY - 1996 DA - 1996// TI - Pseudogenes in ribonuclease evolution: a source of new biomacromolecular function? JO - FEBS Lett VL - 382 UR - https://doi.org/10.1016/0014-5793(96)00191-3 DO - 10.1016/0014-5793(96)00191-3 ID - Trabesinger-Ruef1996 ER - TY - JOUR AU - Wakeley, J. PY - 1996 DA - 1996// TI - The variance of pairwise nucleotide differences in two populations with migration JO - Theor Popul Biol VL - 49 UR - https://doi.org/10.1006/tpbi.1996.0002 DO - 10.1006/tpbi.1996.0002 ID - Wakeley1996 ER - TY - JOUR AU - Bennetzen, J. L. AU - Hall, B. D. PY - 1982 DA - 1982// TI - Codon selection in yeast JO - J Biol Chem VL - 257 ID - Bennetzen1982 ER - TY - JOUR AU - Lawrence, J. G. AU - Ochman, H. PY - 1998 DA - 1998// TI - Molecular archaeology of the Escherichia coli genome JO - Proc Natl Acad Sci U S A VL - 95 UR - https://doi.org/10.1073/pnas.95.16.9413 DO - 10.1073/pnas.95.16.9413 ID - Lawrence1998 ER - TY - CHAP AU - Jukes, T. H. AU - Cantor, C. R. ED - Munro, H. N. PY - 1969 DA - 1969// TI - Evolution of protein molecules. BT - Mammalian Protein Metabolism, UR - https://doi.org/10.1016/B978-1-4832-3211-9.50009-7 DO - 10.1016/B978-1-4832-3211-9.50009-7 ID - Jukes1969 ER - TY - CHAP AU - Atkins, P. AU - de Paula, J. PY - 2002 DA - 2002// BT - Elements of Physical Chemistry with Applications in Biology PB - New York CY - Freeman ID - Atkins2002 ER - TY - JOUR AU - Gillespie, J. H. PY - 1986 DA - 1986// TI - Rates of Molecular Evolution JO - Ann Rev Ecol Syst VL - 17 UR - https://doi.org/10.1146/annurev.es.17.110186.003225 DO - 10.1146/annurev.es.17.110186.003225 ID - Gillespie1986 ER - TY - JOUR AU - Cutler, D. J. PY - 2000 DA - 2000// TI - Estimating divergence times in the presence of an overdispersed molecular clock JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026264 DO - 10.1093/oxfordjournals.molbev.a026264 ID - Cutler2000 ER - TY - JOUR AU - Smith, N. G. AU - Eyre-Walker, A. PY - 2003 DA - 2003// TI - Partitioning the variation in mammalian substitution rates JO - Mol Biol Evol VL - 20 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004231 DO - 10.1093/oxfordjournals.molbev.a004231 ID - Smith2003 ER - TY - JOUR AU - Stajich, J. E. AU - Block, D. AU - Boulez, K. AU - Brenner, S. E. AU - Chervitz, S. A. AU - Dagdigian, C. AU - Fuellen, G. AU - Gilbert, J. G. AU - Korf, I. AU - Lapp, H. AU - Lehvaslaiho, H. AU - Matsalla, C. AU - Mungall, C. J. AU - Osborne, B. I. AU - Pocock, M. R. AU - Schattner, P. AU - Senger, M. AU - Stein, L. D. AU - Stupka, E. AU - Wilkinson, M. D. AU - Birney, E. PY - 2002 DA - 2002// TI - The Bioperl toolkit: Perl modules for the life sciences JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.361602 DO - 10.1101/gr.361602 ID - Stajich2002 ER - TY - CHAP AU - Gonnet, G. H. AU - Benner, S. A. PY - 1991 DA - 1991// BT - Computational Biochemistry Resarch at ETH. Technical Report 154 ID - Gonnet1991 ER - TY - JOUR AU - Gonnet, G. H. AU - Cohen, M. A. AU - Benner, S. A. PY - 1992 DA - 1992// TI - Exhaustive matching of the entire protein sequence database JO - Science VL - 256 UR - https://doi.org/10.1126/science.1604319 DO - 10.1126/science.1604319 ID - Gonnet1992 ER -