Stuart J Macdonald

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Prospects for identifying functional variation across the genome
    Stuart J Macdonald
    Department of Ecology and Evolutionary Biology, University of California, Irvine, 92697 2525, USA
    Proc Natl Acad Sci U S A 102:6614-21. 2005
  2. pmc Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura
    Stuart J Macdonald
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    Genome Biol 7:R67. 2006
  3. pmc A low-cost open-source SNP genotyping platform for association mapping applications
    Stuart J Macdonald
    Department of Ecology and Evolutionary Biology, University of California Irvine, CA 92697 2525, USA
    Genome Biol 6:R105. 2005
  4. pmc The effect of polymorphisms in the enhancer of split gene complex on bristle number variation in a large wild-caught cohort of Drosophila melanogaster
    Stuart J Macdonald
    Department of Ecology and Evolutionary Biology, University of California Irvine, 321 Steinhaus Hall, Irvine, CA 92697 2525, USA
    Genetics 171:1741-56. 2005
  5. ncbi request reprint Identifying signatures of selection at the enhancer of split neurogenic gene complex in Drosophila
    Stuart J Macdonald
    Department of Ecology and Evolutionary Biology, University of California, Irvine, USA
    Mol Biol Evol 22:607-19. 2005
  6. pmc A potential regulatory polymorphism upstream of hairy is not associated with bristle number variation in wild-caught Drosophila
    Stuart J Macdonald
    Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697 2525, USA
    Genetics 167:2127-31. 2004
  7. pmc How repeatable are associations between polymorphisms in achaete-scute and bristle number variation in Drosophila?
    Jonathan D Gruber
    Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA
    Genetics 175:1987-97. 2007
  8. pmc Joint estimates of quantitative trait locus effect and frequency using synthetic recombinant populations of Drosophila melanogaster
    Stuart J Macdonald
    Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA
    Genetics 176:1261-81. 2007
  9. pmc Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource
    Elizabeth G King
    Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
    Genome Res 22:1558-66. 2012
  10. pmc Properties and power of the Drosophila Synthetic Population Resource for the routine dissection of complex traits
    Elizabeth G King
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Genetics 191:935-49. 2012

Collaborators

Detail Information

Publications14

  1. pmc Prospects for identifying functional variation across the genome
    Stuart J Macdonald
    Department of Ecology and Evolutionary Biology, University of California, Irvine, 92697 2525, USA
    Proc Natl Acad Sci U S A 102:6614-21. 2005
    ..If these methods collectively identify the majority of functional noncoding polymorphisms, genotyping only these SNPs in an association mapping framework would reduce genotyping effort for noncoding regions 4-fold...
  2. pmc Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura
    Stuart J Macdonald
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    Genome Biol 7:R67. 2006
    ..Any survey of genomic variation is incomplete without an assessment of structural changes...
  3. pmc A low-cost open-source SNP genotyping platform for association mapping applications
    Stuart J Macdonald
    Department of Ecology and Evolutionary Biology, University of California Irvine, CA 92697 2525, USA
    Genome Biol 6:R105. 2005
    ..The cost-effective, open-source nature of our methodology may make it particularly attractive to those working in nonmodel systems...
  4. pmc The effect of polymorphisms in the enhancer of split gene complex on bristle number variation in a large wild-caught cohort of Drosophila melanogaster
    Stuart J Macdonald
    Department of Ecology and Evolutionary Biology, University of California Irvine, 321 Steinhaus Hall, Irvine, CA 92697 2525, USA
    Genetics 171:1741-56. 2005
    ..It may not be straightforward to extend the results of laboratory-based association studies to natural populations...
  5. ncbi request reprint Identifying signatures of selection at the enhancer of split neurogenic gene complex in Drosophila
    Stuart J Macdonald
    Department of Ecology and Evolutionary Biology, University of California, Irvine, USA
    Mol Biol Evol 22:607-19. 2005
    ..All sites in regions apparently visible to various selective forces are candidates for future work to determine their phenotypic effects...
  6. pmc A potential regulatory polymorphism upstream of hairy is not associated with bristle number variation in wild-caught Drosophila
    Stuart J Macdonald
    Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697 2525, USA
    Genetics 167:2127-31. 2004
    ..Despite >90% power to detect effects as low as 0.27 bristles (<1% of the total variation in bristle number) we did not replicate the association in nature. Potential explanations for this result are explored...
  7. pmc How repeatable are associations between polymorphisms in achaete-scute and bristle number variation in Drosophila?
    Jonathan D Gruber
    Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA
    Genetics 175:1987-97. 2007
    ..Nevertheless, inconsistent results from the other three panels suggest that the relationship between polymorphic genetic markers and loci contributing to continuous variation is not a simple one...
  8. pmc Joint estimates of quantitative trait locus effect and frequency using synthetic recombinant populations of Drosophila melanogaster
    Stuart J Macdonald
    Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA
    Genetics 176:1261-81. 2007
    ..Models that seek to explain the maintenance of genetic variation make different predictions about the population frequency of QTL alleles. Thus, mapping QTL in eight-way recombinant populations can distinguish between these models...
  9. pmc Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource
    Elizabeth G King
    Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
    Genome Res 22:1558-66. 2012
    ..The DSPR represents an important step toward the ultimate goal of a complete understanding of the genetics of complex traits in the Drosophila model system...
  10. pmc Properties and power of the Drosophila Synthetic Population Resource for the routine dissection of complex traits
    Elizabeth G King
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Genetics 191:935-49. 2012
    ..We found the DSPR has both high power (e.g., 84% power to detect a 5% QTL) and high mapping resolution (e.g., ∼1.5 cM for a 5% QTL)...
  11. pmc The Genetic Architecture of Methotrexate Toxicity Is Similar in Drosophila melanogaster and Humans
    Galina Kislukhin
    Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California 92697 2525
    G3 (Bethesda) 3:1301-10. 2013
    ..melanogaster as a model for uncovering the genetic basis of chemotoxicity and suggest the genetic basis of MTX toxicity is due to a handful of genes each harboring multiple segregating regulatory factors. ..
  12. pmc Abundance and Distribution of Transposable Elements in Two Drosophila QTL Mapping Resources
    Julie M Cridland
    Department of Ecology, Evolution and Physiology, University of California, Irvine
    Mol Biol Evol 30:2311-27. 2013
    ..Our data suggest that "burden tests" that test for the effect of TEs as a class may be more fruitful. ..
  13. ncbi request reprint Genome-wide transcript profiles in aging and calorically restricted Drosophila melanogaster
    Scott D Pletcher
    Department of Biology, University College London, The Darwin Building, Gower Street, London WC1E 6BT, UK
    Curr Biol 12:712-23. 2002
    ..We used the global patterns of expression profiles to test if particular genomic regions contribute differentially to changes in transcript profiles with age and if global disregulation of gene expression occurs during aging...
  14. pmc Selection and evaluation of tagging SNPs in the neuronal-sodium-channel gene SCN1A: implications for linkage-disequilibrium gene mapping
    Mike E Weale
    The Centre for Genetic Anthropology, Department of Biology, London, United Kingdom
    Am J Hum Genet 73:551-65. 2003
    ..This could significantly complicate tagging approaches for phenotypes influenced by variants that have experienced positive selection...