Searching journal content for articles similar to Gaffney and Keightley 15 (8): 1086.

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  1. Research: Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
    • David Thybert,
    • Maša Roller,
    • Fábio C.P. Navarro,
    • Ian Fiddes,
    • Ian Streeter,
    • Christine Feig,
    • David Martin-Galvez,
    • Mikhail Kolmogorov,
    • Václav Janoušek,
    • Wasiu Akanni,
    • Bronwen Aken,
    • Sarah Aldridge,
    • Varshith Chakrapani,
    • William Chow,
    • Laura Clarke,
    • Carla Cummins,
    • Anthony Doran,
    • Matthew Dunn,
    • Leo Goodstadt,
    • Kerstin Howe,
    • Matthew Howell,
    • Ambre-Aurore Josselin,
    • Robert C. Karn,
    • Christina M. Laukaitis,
    • Lilue Jingtao,
    • Fergal Martin,
    • Matthieu Muffato,
    • Stefanie Nachtweide,
    • Michael A. Quail,
    • Cristina Sisu,
    • Mario Stanke,
    • Klara Stefflova,
    • Cock Van Oosterhout,
    • Frederic Veyrunes,
    • Ben Ward,
    • Fengtang Yang,
    • Golbahar Yazdanifar,
    • Amonida Zadissa,
    • David J. Adams,
    • Alvis Brazma,
    • Mark Gerstein,
    • Benedict Paten,
    • Son Pham,
    • Thomas M. Keane,
    • Duncan T. Odom,
    • and Paul Flicek
    Genome Res. April 2018 28: 448-459; Published in Advance March 21, 2018, doi:10.1101/gr.234096.117
    ...lineage-specific characteristics (Kim et al. 2011; Wu et al. 2014; Foote et al. 2015). Indeed, evolutionary comparisons have even enabled the identification of genomic variation, such as repeat expansions, which can explain aspects of and karyotype evolution (Carbone et al. 2014).Even closely related...
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  2. Research: The mutational spectrum of non-CpG DNA varies with CpG content
    • Jean-Claude Walser and
    • Anthony V. Furano
    Genome Res. July 2010 20: 875-882; Published in Advance May 24, 2010, doi:10.1101/gr.103283.109
    ...Sciences (ELS). John Wiley, Chichester, UK. doi: 10.1002/ 9780470015902.a0021740. Gaffney DJ, Keightley PD. 2005. The scale of mutational variation in the murid . Genome Res 15: 1086–1094. Gaffney DJ, Keightley PD. 2008. Effect of the assignment of ancestral CpG state on the estimation of nucleotide...
  3. Review: What fraction of the human genome is functional?
    • Chris P. Ponting and
    • Ross C. Hardison
    Genome Res. November 2011 21: 1769-1776; Published in Advance August 29, 2011, doi:10.1101/gr.116814.110
    ...and identifies key regulatory elements in the a globin cluster. Hum Mol Genet 10: 371–382. Gaffney DJ, Keightley PD. 2005. The scale of mutational variation in the murid . Genome Res 15: 1086–1094. Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X. 2009. Identifying novel constrained elements...
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  4. LETTER: Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison
    • Daniel L. Halligan and
    • Peter D. Keightley
    Genome Res. July 2006 16: 875-884; Published in Advance June 2, 2006, doi:10.1101/gr.5022906
    ...estimated constraint using an unconstrained standard from the same section of the in order to account for large-scale variation in the mutation rate. We identified two classes of putatively unconstrained sequence (the fastest evolving intronic [FEI] sites and the fastest evolving fourfold degenerate [FEF...
  5. LETTER: The genome-wide determinants of human and chimpanzee microsatellite evolution
    • Yogeshwar D. Kelkar,
    • Svitlana Tyekucheva,
    • Francesca Chiaromonte,
    • and Kateryna D. Makova
    Genome Res. January 2008 18: 30-38; Published in Advance November 21, 2007, doi:10.1101/gr.7113408
    ..., these features have not been considered together or on a -wide scale. Genomic features varying regionally are also expected to contribute to variation in microsatellite mutation rates ( Ellegren 2004 ). High local substitution rates cause frequent repeat interruptions that make slippage less likely and decrease...
  6. RESOURCE: Initial sequence and comparative analysis of the cat genome
    • Joan U. Pontius,
    • James C. Mullikin,
    • Douglas R. Smith,
    • Agencourt Sequencing Team,
    • Kerstin Lindblad-Toh,
    • Sante Gnerre,
    • Michele Clamp,
    • Jean Chang,
    • Robert Stephens,
    • Beena Neelam,
    • Natalia Volfovsky,
    • Alejandro A. Schäffer,
    • Richa Agarwala,
    • Kristina Narfström,
    • William J. Murphy,
    • Urs Giger,
    • Alfred L. Roca,
    • Agostinho Antunes,
    • Marilyn Menotti-Raymond,
    • Naoya Yuhki,
    • Jill Pecon-Slattery,
    • Warren E. Johnson,
    • Guillaume Bourque,
    • Glenn Tesler,
    • NISC Comparative Sequencing Program,
    • and Stephen J. O’Brien
    Genome Res. November 2007 17: 1675-1689; doi:10.1101/gr.6380007
    ...; Supplemental Table S4). These results reflect the well-known interchromosomal reshuffling of murid and canine organization relative to the more conserved disposition in the human (primate) or cat (Felidae) genomic history ( O’Brien et al. 1999 ; Bourque et al. 2004 ; Murphy et al. 2004 , 2005 ). The apparent...
  7. LETTER: Retroposed Copies of the HMG Genes: A Window to Genome Dynamics
    • Liora Z. Strichman-Almashanu,
    • Michael Bustin,
    • and David Landsman
    Genome Res. May 1, 2003 13: 800-812; doi:10.1101/gr.893803
    ...the boxes) intervening genomic DNA, or introns if colored; (–//–) a break artificially inserted into the long sequence for convenient display. Figure not drawn to scale. The base composition was calculated for 500 bp flanking the RPCs and was found to be AT-rich (Table 2 ). The 3′-flanking sequence average...
  8. LETTER: Biased clustered substitutions in the human genome: The footprints of male-driven biased gene conversion
    • Timothy R. Dreszer,
    • Gregory D. Wall,
    • David Haussler,
    • and Katherine S. Pollard
    Genome Res. October 2007 17: 1420-1430; Published in Advance September 4, 2007, doi:10.1101/gr.6395807
    ...-blooded vertebrate s as large as ∼300 kb with strikingly greater or lesser proportions of G+C than surrounding areas ( Bernardi et al. 1985 ; Bernardi 2000 ). Three main theories have been proposed to explain the existence of isochores ( Eyre-Walker and Hurst 2001 ). The first involves variation in mutation rates...
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  9. LETTER: Comparative Evolutionary Genomics of Androgen-Binding Protein Genes
    • Richard D. Emes,
    • Matthew C. Riley,
    • Christina M. Laukaitis,
    • Leo Goodstadt,
    • Robert C. Karn,
    • and Chris P. Ponting
    Genome Res. August 2004 14: 1516-1529; Published in Advance July 15, 2004, doi:10.1101/gr.2540304
    ...are more influenced by variation in Abpbg -like genes. We propose a role for ABPα/β/γ proteins as pheromones, or in modulating odorant detection. This would account for the extraordinary adaptive evolution of these genes, and surrounding genomic regions, in murid rodents. Footnotes...
  10. Method: Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease
    • Yi-Fei Huang and
    • Adam Siepel
    Genome Res. August 2019 29: 1310-1321; Published in Advance June 27, 2019, doi:10.1101/gr.245522.118
    ...in the central nervous system or associated with autism spectrum disorder, as well as 773 genes under unusually weak selection, which tend to be associated with metabolism. This combination of classical population genetic theory with modern machine-learning and large-scale genomic data is a powerful paradigm...
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