Searching journal content for articles similar to Murphy et al. 17 (4): 000.

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  1. Method: Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis
    • John E. McCormack,
    • Brant C. Faircloth,
    • Nicholas G. Crawford,
    • Patricia Adair Gowaty,
    • Robb T. Brumfield,
    • and Travis C. Glenn
    Genome Res. April 2012 22: 746-754; Published in Advance December 29, 2011, doi:10.1101/gr.125864.111
    ...Faircloth N.G. Crawford Travis C Glenn John McCormack Crawford, N.G T Glenn T.C. Glenn genome;gr.125864.111 10.1101/gr.125864.111 1088-9051 Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis Method Ultraconserved elements...
  2. Letter: Mosaic retroposon insertion patterns in placental mammals
    • Gennady Churakov,
    • Jan Ole Kriegs,
    • Robert Baertsch,
    • Anja Zemann,
    • Jürgen Brosius,
    • and Jürgen Schmitz
    Genome Res. May 2009 19: 868-875; Published in Advance March 4, 2009, doi:10.1101/gr.090647.108
    ...the root of the placental mammal phylogeny. Genome Res. 17: 413–421. Nikolaev, S., Montoya-Burgos, J.I., Margulies, E.H., Rougemont, J., Nyffeler, B., and Antonarakis, S.E. 2007. Early history of mammals is elucidated with the ENCODE multiple species sequencing data. PLoS Genet. 3: e2. doi: 10.1371/journal...
  3. PERSPECTIVE: The opossum genome: Insights and opportunities from an alternative mammal
    • Paul B. Samollow
    Genome Res. August 2008 18: 1199-1215; doi:10.1101/gr.065326.107
    ...The opossum genome: Insights and opportunities from an alternative mammal Paul B. Samollow 1 Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences,Texas A&M University, College Station, Texas 77843-4458, USA...
  4. Mini-Review: Toward telomere-to-telomere cat genomes for precision medicine and conservation biology
    • William J. Murphy and
    • Andrew J. Harris
    Genome Res. May 2024 34: 655-664; Published in Advance June 7, 2024, doi:10.1101/gr.278546.123
    ..., Fel d 1. CRISPR J 5: 213–223. doi:10.1089/crispr.2021.0101 ↵Brannan EO, Hartley GA, O'Neill RJ. 2024. Mechanisms of rapid karyotype evolution in mammals. Genes (Basel) 15: 62. doi:10.3390/genes15010062 ↵Brashear WA, Bredemeyer KR, Murphy WJ. 2021. Genomic architecture constrained placental mammal X...
  5. Research: Massive turnover of functional sequence in human and other mammalian genomes
    • Stephen Meader,
    • Chris P. Ponting,
    • and Gerton Lunter
    Genome Res. October 2010 20: 1335-1343; Published in Advance August 6, 2010, doi:10.1101/gr.108795.110
    ...biological function, and second, are apparent differences in organismal complexity reflected in an objective measure of genomic complexity? Here, we address both questions by applying, across the mammalian phylogeny, an evolutionary model that estimates the amount of functional DNA that is shared between two...
    OPEN ACCESS ARTICLE
  6. Perspective: Phylogenomics of primates and their ancestral populations
    • Adam Siepel
    Genome Res. November 2009 19: 1929-1941; Published in Advance October 3, 2009, doi:10.1101/gr.084228.108
    ...), to identify and characterize functional sequences present in primates but not other mammals (Boffelli et al. 2003), and to catalog the genomic similarities and differences between humans and nonhuman primates widely used in biomedical research, such as the baboon and rhesus macaque (Rhesus Macaque Genome...
  7. LETTER: Evolution of the mammalian transcription factor binding repertoire via transposable elements
    • Guillaume Bourque,
    • Bernard Leong,
    • Vinsensius B. Vega,
    • Xi Chen,
    • Yen Ling Lee,
    • Kandhadayar G. Srinivasan,
    • Joon-Lin Chew,
    • Yijun Ruan,
    • Chia-Lin Wei,
    • Huck Hui Ng,
    • and Edison T. Liu
    Genome Res. November 2008 18: 1752-1762; Published in Advance August 5, 2008, doi:10.1101/gr.080663.108
    ...-Lin Chew 2 , Yijun Ruan 3 , Chia-Lin Wei 3 , Huck Hui Ng 2 , and Edison T. Liu 4 1 Computational and Mathematical Biology, Genome Institute of Singapore, Singapore 138672, Singapore; 2 Stem Cell and Developmental Biology, Genome...
  8. RESOURCE: Development and application of a phylogenomic toolkit: Resolving the evolutionary history of Madagascar’s lemurs
    • Julie E. Horvath,
    • David W. Weisrock,
    • Stephanie L. Embry,
    • Isabella Fiorentino,
    • James P. Balhoff,
    • Peter Kappeler,
    • Gregory A. Wray,
    • Huntington F. Willard,
    • and Anne D. Yoder
    Genome Res. March 2008 18: 489-499; Published in Advance February 1, 2008, doi:10.1101/gr.7265208
    ...as the sister lineage to all other primates. Previous attempts to resolve the phylogeny of lemurs employed limited mitochondrial or small nuclear data sets, with many relationships poorly supported or entirely unresolved. We used genomic resources to develop 11 novel markers from nine chromosomes, representing...
  9. Research: Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus
    • Julie E. Horvath,
    • Christina B. Sheedy,
    • Stephanie L. Merrett,
    • Abdoulaye Banire Diallo,
    • David L. Swofford,
    • NISC Comparative Sequencing Program,
    • Eric D. Green,
    • and Huntington F. Willard
    Genome Res. June 2011 21: 850-862; Published in Advance April 25, 2011, doi:10.1101/gr.111849.110
    ...sampling from the evolutionary tree, comparative genomics is a powerful approach for understanding evolutionary changes in architecture and their potential implications for function. Multispecies sequence comparisons among placental mammals have allowed identification of lineage-specific elements (Boffelli...
  10. Letter: Ecological adaptation determines functional mammalian olfactory subgenomes
    • Sara Hayden,
    • Michaël Bekaert,
    • Tess A. Crider,
    • Stefano Mariani,
    • William J. Murphy,
    • and Emma C. Teeling
    Genome Res. January 2010 20: 1-9; Published in Advance December 1, 2009, doi:10.1101/gr.099416.109
    ...OR gene repertoires from 50 mammalian genomes. We amplified more than 2000 OR genes in aquatic, semi-aquatic, and flying mammals and coupled these data with 48,000 OR genes from mostly terrestrial mammals, extracted from genomic projects. Phylogenomic, Bayesian assignment, and principle component analyses...
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