Searching journal content for articles similar to Yang et al. 14 (4): 517.

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  1. Research: Less effective selection leads to larger genomes
    • Tristan Lefébure,
    • Claire Morvan,
    • Florian Malard,
    • Clémentine François,
    • Lara Konecny-Dupré,
    • Laurent Guéguen,
    • Michèle Weiss-Gayet,
    • Andaine Seguin-Orlando,
    • Luca Ermini,
    • Clio Der Sarkissian,
    • N. Pierre Charrier,
    • David Eme,
    • Florian Mermillod-Blondin,
    • Laurent Duret,
    • Cristina Vieira,
    • Ludovic Orlando,
    • and Christophe Jean Douady
    Genome Res. June 2017 27: 1016-1028; Published in Advance April 19, 2017, doi:10.1101/gr.212589.116
    ..., predictions of the MH hypothesis can vary in opposite directions depending on the underlying pattern of indel mutations. In eukaryotes, where indel mutation patterns are typically biased toward insertions, reductions in population size are predicted to lead to increasing GS. Conversely, similar Ne reductions...
  2. LETTER: Occurrence and Consequences of Coding Sequence Insertions and Deletions in Mammalian Genomes
    • Martin S. Taylor,
    • Chris P. Ponting,
    • and Richard R. Copley
    Genome Res. April 2004 14: 555-566; doi:10.1101/gr.1977804
    ...that had previously been shown to have orthologous 1:1:1 relationships between mouse, rat, and human ( Rat Genome Sequencing Project Consortium 2004 ). We identified high-quality regions of alignments that included an insertion or deletion in either of the rodent sequences (see Methods). Only indel events...
  3. ARTICLE: Comparative Recombination Rates in the Rat, Mouse, and Human Genomes
    • Michael I. Jensen-Seaman,
    • Terrence S. Furey,
    • Bret A. Payseur,
    • Yontao Lu,
    • Krishna M. Roskin,
    • Chin-Fu Chen,
    • Michael A. Thomas,
    • David Haussler,
    • and Howard J. Jacob
    Genome Res. April 2004 14: 528-538; doi:10.1101/gr.1970304
    ...-specific estimates of substitution, and that utilize node-specific estimates of recombination will have substantially greater power to detect such patterns compared to simple human–mouse comparisons. Therefore, our rat–mouse–human comparative approach provides a beginning toward what will be a much more complete...
  4. ARTICLE: Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution
    • Ross C. Hardison,
    • Krishna M. Roskin,
    • Shan Yang,
    • Mark Diekhans,
    • W. James Kent,
    • Ryan Weber,
    • Laura Elnitski,
    • Jia Li,
    • Michael O'Connor,
    • Diana Kolbe,
    • Scott Schwartz,
    • Terrence S. Furey,
    • Simon Whelan,
    • Nick Goldman,
    • Arian Smit,
    • Webb Miller,
    • Francesca Chiaromonte,
    • and David Haussler
    Genome Res. January 1, 2003 13: 13-26; doi:10.1101/gr.844103
    ...Goldman, N A Smit Michael, O'Connor Simon S Yang T Furey KM Roskin Goldman, Nick 1549-5469 1088-9051 10.1101/gr.844103 genome;13/1/13 Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution Covariation in Frequencies of Substitution, Deletion...
  5. LETTER: Insertions and Deletions Are Male Biased Too: A Whole-Genome Analysis in Rodents
    • Kateryna D. Makova,
    • Shan Yang,
    • and Francesca Chiaromonte
    Genome Res. April 2004 14: 567-573; doi:10.1101/gr.1971104
    ...-to-female ratio of the number of germline cell divisions in rat and mouse. Thus, this is consistent with nucleotide substitutions and small indels occurring primarily during DNA replication. Footnotes Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1971104. ↵ 6...
  6. Method: New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes
    • Brian J. Parker,
    • Ida Moltke,
    • Adam Roth,
    • Stefan Washietl,
    • Jiayu Wen,
    • Manolis Kellis,
    • Ronald Breaker,
    • and Jakob Skou Pedersen
    Genome Res. November 2011 21: 1929-1943; Published in Advance October 12, 2011, doi:10.1101/gr.112516.110
    ...double substitutions (e.g., AU 4 GC) and compatible single substitutions (e.g., AU4 GU). EvoFold, and related programs (Rivas and Eddy 2001; Washietl et al. 2005), detect this signal by analyzing the substitution pattern along genomic alignments and use it to identify these conserved RNA structures...
  7. Research: The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are important
    • Erika M. Kvikstad and
    • Kateryna D. Makova
    Genome Res. May 2010 20: 600-613; Published in Advance March 10, 2010, doi:10.1101/gr.099044.109
    ...element density, respectively. Second, we analyze sex chromosome versus autosome TE densities corrected for regional genomic effects. We discover that sex-chromosome bias in Alu and L1 distributions not only persists after accounting for these effects, but even presents differences in patterns...
  8. ARTICLE: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    • Adam Siepel,
    • Gill Bejerano,
    • Jakob S. Pedersen,
    • Angie S. Hinrichs,
    • Minmei Hou,
    • Kate Rosenbloom,
    • Hiram Clawson,
    • John Spieth,
    • LaDeana W. Hillier,
    • Stephen Richards,
    • George M. Weinstock,
    • Richard K. Wilson,
    • Richard A. Gibbs,
    • W. James Kent,
    • Webb Miller,
    • and David Haussler
    Genome Res. August 2005 15: 1034-1050; Published in Advance July 15, 2005, doi:10.1101/gr.3715005
    ..., Houston, Texas 77030, USA Abstract We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu rubripes ). Parallel searches have been performed with multiple...
  9. LETTER: Characterization of Evolutionary Rates and Constraints in Three Mammalian Genomes
    • Gregory M. Cooper,
    • Michael Brudno,
    • Eric A. Stone,
    • Inna Dubchak,
    • Serafim Batzoglou,
    • and Arend Sidow
    Genome Res. April 2004 14: 539-548; doi:10.1101/gr.2034704
    ...constitute independent sites. Using these data sets, we describe the patterns and rates of various microevolutionary features, such as point substitutions, insertions, and deletions, along all three branches of the unrooted tree that relates human, mouse, and rat. We furthermore estimate rates of evolution...
  10. LETTER: Identification of Evolutionary Hotspots in the Rodent Genomes
    • Von Bing Yap and
    • Lior Pachter
    Genome Res. April 2004 14: 574-579; doi:10.1101/gr.1967904
    .... Patterns of insertions and their covariation with substitutions in the rat, mouse and human s. Genome Res. (this issue). ↵ Yang, Z. 1994 . Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39 : 105 -111. Yap, V.B. and Speed, T.P. 2004 . Modeling DNA base substitution in large genomic regions...
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