Hunter B Fraser

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression
    Ana Ariza-Cosano
    Centro Andaluz de Biologia del Desarrollo CABD, CSIC Universidad Pablo de Olavide Junta de AndalucĂ­a, Ctra Utrera km 1, Seville 41013, Spain
    BMC Genomics 13:713. 2012
  2. pmc Gene expression drives local adaptation in humans
    Hunter B Fraser
    Department of Biology, Stanford University, Stanford, California 94305, USA
    Genome Res 23:1089-96. 2013
  3. pmc Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity
    Hunter B Fraser
    Department of Biology, Stanford University, Stanford, California 94305, USA
    Genome Res 22:1930-9. 2012
  4. pmc Population-specificity of human DNA methylation
    Hunter B Fraser
    Department of Biology, Stanford University, Stanford, CA 94305, USA
    Genome Biol 13:R8. 2012
  5. pmc Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation
    Tomas Babak
    Rosetta Inpharmatics, LLC, 401 Terry Ave N, Seattle, WA 98109, USA
    BMC Genomics 11:473. 2010
  6. pmc The quantitative genetics of phenotypic robustness
    Hunter B Fraser
    Department of Biology, Stanford University, Stanford, California, USA
    PLoS ONE 5:e8635. 2010
  7. pmc Evidence for widespread adaptive evolution of gene expression in budding yeast
    Hunter B Fraser
    Department of Biology, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 107:2977-82. 2010
  8. doi request reprint Genome-wide approaches to the study of adaptive gene expression evolution: systematic studies of evolutionary adaptations involving gene expression will allow many fundamental questions in evolutionary biology to be addressed
    Hunter B Fraser
    Department of Biology, Stanford University, Stanford, CA, USA
    Bioessays 33:469-77. 2011
  9. pmc Systematic detection of polygenic cis-regulatory evolution
    Hunter B Fraser
    Rosetta Inpharmatics, Seattle, Washington, United States of America
    PLoS Genet 7:e1002023. 2011
  10. ncbi request reprint Assessing the determinants of evolutionary rates in the presence of noise
    Joshua B Plotkin
    Department of Biology, The University of Pennsylvania, USA
    Mol Biol Evol 24:1113-21. 2007

Detail Information

Publications17

  1. pmc Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression
    Ana Ariza-Cosano
    Centro Andaluz de Biologia del Desarrollo CABD, CSIC Universidad Pablo de Olavide Junta de AndalucĂ­a, Ctra Utrera km 1, Seville 41013, Spain
    BMC Genomics 13:713. 2012
    ..While isolated examples of trans-changes have been identified, the scale of their overall contribution to regulatory and phenotypic evolution remains unclear...
  2. pmc Gene expression drives local adaptation in humans
    Hunter B Fraser
    Department of Biology, Stanford University, Stanford, California 94305, USA
    Genome Res 23:1089-96. 2013
    ..These results provide the first examples of polygenic gene expression adaptation in humans, as well as the first genome-scale support for the hypothesis that changes in gene expression have driven human adaptation...
  3. pmc Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity
    Hunter B Fraser
    Department of Biology, Stanford University, Stanford, California 94305, USA
    Genome Res 22:1930-9. 2012
    ..These results suggest that cis-regulatory adaptation can occur at the level of physically interacting modules and that one such polygenic adaptation led to increased virulence during the evolution of a pathogenic yeast...
  4. pmc Population-specificity of human DNA methylation
    Hunter B Fraser
    Department of Biology, Stanford University, Stanford, CA 94305, USA
    Genome Biol 13:R8. 2012
    ..In addition, whether the genetic control of polymorphic DNA methylation is population-specific has not been investigated...
  5. pmc Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation
    Tomas Babak
    Rosetta Inpharmatics, LLC, 401 Terry Ave N, Seattle, WA 98109, USA
    BMC Genomics 11:473. 2010
    ....
  6. pmc The quantitative genetics of phenotypic robustness
    Hunter B Fraser
    Department of Biology, Stanford University, Stanford, California, USA
    PLoS ONE 5:e8635. 2010
    ..These preliminary results suggest that naturally occurring polymorphisms affecting phenotypic robustness could be abundant, and that these polymorphisms may generally buffer either genetic or environmental variation, but not both...
  7. pmc Evidence for widespread adaptive evolution of gene expression in budding yeast
    Hunter B Fraser
    Department of Biology, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 107:2977-82. 2010
    ....
  8. doi request reprint Genome-wide approaches to the study of adaptive gene expression evolution: systematic studies of evolutionary adaptations involving gene expression will allow many fundamental questions in evolutionary biology to be addressed
    Hunter B Fraser
    Department of Biology, Stanford University, Stanford, CA, USA
    Bioessays 33:469-77. 2011
    ..Systematic studies such as these will allow a number of key questions currently facing the field of gene expression evolution to be addressed...
  9. pmc Systematic detection of polygenic cis-regulatory evolution
    Hunter B Fraser
    Rosetta Inpharmatics, Seattle, Washington, United States of America
    PLoS Genet 7:e1002023. 2011
    ..These coordinated adaptations may contribute to divergence in a wide range of morphological, physiological, and behavioral phenotypes...
  10. ncbi request reprint Assessing the determinants of evolutionary rates in the presence of noise
    Joshua B Plotkin
    Department of Biology, The University of Pennsylvania, USA
    Mol Biol Evol 24:1113-21. 2007
    ..More accurate measurements or more sophisticated statistical techniques will be required to determine which one, if any, of these factors dominates protein evolution...
  11. pmc Predictive genes in adjacent normal tissue are preferentially altered by sCNV during tumorigenesis in liver cancer and may rate limiting
    John R Lamb
    Rosetta Inpharmatics, LLC, Seattle, Washington, United States of America
    PLoS ONE 6:e20090. 2011
    ..The relationships between these two sets of predictive genes and the general process of tumorigenesis and disease progression remains unclear...
  12. pmc Functional genomic analysis of the rates of protein evolution
    Dennis P Wall
    Department of Biological Sciences, and Stanford Genome Technology Center, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 102:5483-8. 2005
    ....
  13. pmc Conservation and evolution of cis-regulatory systems in ascomycete fungi
    Audrey P Gasch
    Genome Sciences Department, Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    PLoS Biol 2:e398. 2004
    ..Our results suggest that the DNA binding specificity of these proteins has coevolved with the sequences found upstream of the Rpn4p target genes and suggest that Rpn4p has a different function in N. crassa...
  14. ncbi request reprint Codon usage and selection on proteins
    Joshua B Plotkin
    Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
    J Mol Evol 63:635-53. 2006
    ..We also discuss several confounding factors, neglected by the Fisher-Wright model, that may limit the applicability of volatility in practice...
  15. pmc Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints
    Manuel Irimia
    Department of Biology, Stanford University, Stanford, California 94305, USA
    Genome Res 22:2356-67. 2012
    ....
  16. pmc Aging and gene expression in the primate brain
    Hunter B Fraser
    Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
    PLoS Biol 3:e274. 2005
    ....
  17. ncbi request reprint Adjusting for selection on synonymous sites in estimates of evolutionary distance
    Aaron E Hirsh
    Department of Biological Sciences, Stanford University, Stanford, California, USA
    Mol Biol Evol 22:174-7. 2005
    ..Here, we use the relationship between codon bias and synonymous divergence observed in four species of the genus Saccharomyces to provide a simple correction for selection on silent sites...