J Madeoy

Summary

Affiliation: University of Washington
Country: USA

Publications

  1. ncbi request reprint TRPV6 exhibits unusual patterns of polymorphism and divergence in worldwide populations
    Joshua M Akey
    Department of Genome Sciences, University of Washington, Seattle, WA 98195 7730, USA
    Hum Mol Genet 15:2106-13. 2006
  2. pmc The evolution of gene expression QTL in Saccharomyces cerevisiae
    James Ronald
    Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
    PLoS ONE 2:e678. 2007
  3. pmc Clusters of adaptive evolution in the human genome
    Laura B Scheinfeldt
    Department of Genome Sciences, University of Washington Seattle, WA, USA
    Front Genet 2:50. 2011
  4. pmc Population Genomics of Intron Splicing in 38 Saccharomyces cerevisiae Genome Sequences
    Daniel A Skelly
    Department of Genome Sciences, University of Washington
    Genome Biol Evol 2009:466-78. 2009
  5. pmc Genome-wide scans for loci under selection in humans
    James Ronald
    University of Washington, Seattle, Washington, USA
    Hum Genomics 2:113-25. 2005
  6. pmc The conserved WW-domain binding sites in Dystroglycan C-terminus are essential but partially redundant for Dystroglycan function
    A S Yatsenko
    Department of Biochemistry, Institute for Stem Cell and Regenerative Medicine, Program in Neurobiology and Behaviour, University of Washington, Seattle, WA 98195, USA
    BMC Dev Biol 9:18. 2009
  7. pmc Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis
    Shameek Biswas
    Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA
    BMC Bioinformatics 9:244. 2008
  8. pmc Constructing genomic maps of positive selection in humans: where do we go from here?
    Joshua M Akey
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Genome Res 19:711-22. 2009
  9. pmc Tracking footprints of artificial selection in the dog genome
    Joshua M Akey
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 107:1160-5. 2010
  10. pmc A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
    Daniel A Skelly
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Genome Res 21:1728-37. 2011

Collaborators

Detail Information

Publications26

  1. ncbi request reprint TRPV6 exhibits unusual patterns of polymorphism and divergence in worldwide populations
    Joshua M Akey
    Department of Genome Sciences, University of Washington, Seattle, WA 98195 7730, USA
    Hum Mol Genet 15:2106-13. 2006
    ..These data strongly suggest that the TRPV6 haplotype defined by the derived alleles at C157R, M378V and M681T conferred a selective advantage that varied spatially, and perhaps temporally, during human history...
  2. pmc The evolution of gene expression QTL in Saccharomyces cerevisiae
    James Ronald
    Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
    PLoS ONE 2:e678. 2007
    ..We also find that essential genes and genes with larger codon bias are subject to slightly stronger cis-regulatory constraint and that positive selection has played a role in the evolution of major trans-acting QTL...
  3. pmc Clusters of adaptive evolution in the human genome
    Laura B Scheinfeldt
    Department of Genome Sciences, University of Washington Seattle, WA, USA
    Front Genet 2:50. 2011
    ....
  4. pmc Population Genomics of Intron Splicing in 38 Saccharomyces cerevisiae Genome Sequences
    Daniel A Skelly
    Department of Genome Sciences, University of Washington
    Genome Biol Evol 2009:466-78. 2009
    ..More generally, our study highlights the advantages of population genomics analyses for exploring the forces that have generated extant patterns of genome variation and for illuminating basic biological processes...
  5. pmc Genome-wide scans for loci under selection in humans
    James Ronald
    University of Washington, Seattle, Washington, USA
    Hum Genomics 2:113-25. 2005
    ..In addition, the paper will highlight several important problems that need to be addressed in future genome-wide studies of natural selection...
  6. pmc The conserved WW-domain binding sites in Dystroglycan C-terminus are essential but partially redundant for Dystroglycan function
    A S Yatsenko
    Department of Biochemistry, Institute for Stem Cell and Regenerative Medicine, Program in Neurobiology and Behaviour, University of Washington, Seattle, WA 98195, USA
    BMC Dev Biol 9:18. 2009
    ..The most C-terminal PPXY motif has been established as a binding site for Dystrophin (Dys) WW-domain. However, our previous studies indicate that both Dystroglycan PPXY motives, WWbsI and WWbsII can bind Dystrophin protein in vitro...
  7. pmc Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis
    Shameek Biswas
    Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA
    BMC Bioinformatics 9:244. 2008
    ..In addition, gene expression traits exhibit a complex correlation structure, which is ignored when analyzing traits individually...
  8. pmc Constructing genomic maps of positive selection in humans: where do we go from here?
    Joshua M Akey
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Genome Res 19:711-22. 2009
    ....
  9. pmc Tracking footprints of artificial selection in the dog genome
    Joshua M Akey
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 107:1160-5. 2010
    ....
  10. pmc A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
    Daniel A Skelly
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Genome Res 21:1728-37. 2011
    ..Our methodology provides a rigorous, quantitative, and high-resolution tool for profiling ASE across whole genomes...
  11. pmc Population genomic analysis of ALMS1 in humans reveals a surprisingly complex evolutionary history
    Laura B Scheinfeldt
    Department of Genome Sciences, University of Washington, Seattle, WA, USA
    Mol Biol Evol 26:1357-67. 2009
    ..These results provide new insights into the evolutionary history of ALMS1 in humans and suggest that selective events identified in genomewide scans may be more complex than currently appreciated...
  12. pmc Gene-expression variation within and among human populations
    John D Storey
    Department of Biostatistics, University of Washington, Seattle, WA 98195 7730, USA
    Am J Hum Genet 80:502-9. 2007
    ..These results provide the first insight into how human population structure manifests itself in gene-expression levels and will help guide the search for regulatory quantitative trait loci...
  13. doi request reprint Inherited variation in gene expression
    Daniel A Skelly
    Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA
    Annu Rev Genomics Hum Genet 10:313-32. 2009
    ..We conclude by discussing the evolution of gene expression levels, and we explore prospects for leveraging new technological developments to investigate inherited variation in gene expression in even greater depth...
  14. pmc Identifying positive selection candidate loci for high-altitude adaptation in Andean populations
    Abigail W Bigham
    Department of Pediatrics, The University of Washington, Seattle, WA 98195, USA
    Hum Genomics 4:79-90. 2009
    ....
  15. pmc Genome-wide insights into the patterns and determinants of fine-scale population structure in humans
    Shameek Biswas
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Am J Hum Genet 84:641-50. 2009
    ....
  16. pmc A genome-wide in vitro bacterial-infection screen reveals human variation in the host response associated with inflammatory disease
    Dennis C Ko
    Department of Immunology, University of Washington, Seattle, WA 98195, USA
    Am J Hum Genet 85:214-27. 2009
    ..These results demonstrate the utility of genome-wide cell-based association screens with microbes in the identification of naturally selected variants that can impact human health...
  17. pmc Population history and natural selection shape patterns of genetic variation in 132 genes
    Joshua M Akey
    Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    PLoS Biol 2:e286. 2004
    ..More generally, our results have important implications for mapping genes underlying complex human diseases...
  18. ncbi request reprint Sequence diversity, natural selection and linkage disequilibrium in the human T cell receptor alpha/delta locus
    Rachel Mackelprang
    Department of Genome Sciences, University of Washington, 357730, Seattle, WA, 98195 7730, USA
    Hum Genet 119:255-66. 2006
    ..Furthermore, we explore signatures of natural selection across V genes. We find evidence of strong directional selection at this locus as evidenced by unusually high values of Fst...
  19. pmc Multiple locus linkage analysis of genomewide expression in yeast
    John D Storey
    Department of Biostatistics, University of Washington, Seattle, Washington, USA
    PLoS Biol 3:e267. 2005
    ..In addition, we show that a two-dimensional scan does not truly allow one to test for simultaneous linkage, and the statistical significance measured from this existing method cannot be interpreted among many traits...
  20. pmc Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays
    James Ronald
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Genome Res 15:284-91. 2005
    ..With this method, we discovered 70 ORFs with evidence for preferential expression of one allele in a diploid hybrid of two S. cerevisiae strains...
  21. pmc Telomere length as a quantitative trait: genome-wide survey and genetic mapping of telomere length-control genes in yeast
    Tonibelle Gatbonton
    Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    PLoS Genet 2:e35. 2006
    ..Furthermore, our results laid the foundation for studying genetic determinants of telomere length-variation and their roles in human disease...
  22. ncbi request reprint High-frequency persistence of an impaired allele of the retroviral defense gene TRIM5alpha in humans
    Sara L Sawyer
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Curr Biol 16:95-100. 2006
    ..The unexpectedly high frequency of an impaired retroviral restriction allele among humans is likely to have a significant impact on our ability to ward off future retroviral challenges...
  23. pmc The genomic architecture of segmental duplications and associated copy number variants in dogs
    Thomas J Nicholas
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Genome Res 19:491-9. 2009
    ..Our results provide insight into mechanisms of canine genome evolution and generate a valuable resource for future evolutionary and phenotypic studies...
  24. ncbi request reprint Genomic insights into positive selection
    Shameek Biswas
    Department of Genome Sciences, University of Washington, 1705 NE Pacific, Seattle, WA 98195, USA
    Trends Genet 22:437-46. 2006
    ....
  25. pmc Genomic signatures of positive selection in humans and the limits of outlier approaches
    Joanna L Kelley
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Genome Res 16:980-9. 2006
    ....

Research Grants10

  1. Heritable variation of mRNA decay rates: An unappreciated source of gene express
    JOSHUA MICHAEL AKEY; Fiscal Year: 2010
    ..This project will provide critical new insights into how genetic variation influences gene expression levels and ultimately the molecular mechanisms of disease. ..
  2. Genome-Wide Analysis of Adaptive Evolution in Humans
    JOSHUA MICHAEL AKEY; Fiscal Year: 2010
    ..Research that increases our understanding of the evolutionary forces that shape patterns of human genetic variation will facilitate disease gene mapping studies. ..
  3. Gene expression variation in geographically diverse human populations
    JOSHUA MICHAEL AKEY; Fiscal Year: 2010
    ..Research that increases our understanding of gene expression variation will facilitate disease gene mapping studies. ..
  4. Gene expression variation in geographically diverse human populations
    Joshua Akey; Fiscal Year: 2009
    ..Research that increases our understanding of gene expression variation will facilitate disease gene mapping studies. ..
  5. Genome-Wide Analysis of Adaptive Evolution in Humans
    Joshua Akey; Fiscal Year: 2007
    ..Research that increases our understanding of the evolutionary forces that shape patterns of human genetic variation will facilitate disease gene mapping studies. ..
  6. Gene expression variation in geographically diverse human populations
    Joshua Akey; Fiscal Year: 2007
    ..Research that increases our understanding of gene expression variation will facilitate disease gene mapping studies. ..
  7. Genome-Wide Analysis of Adaptive Evolution in Humans
    Joshua Akey; Fiscal Year: 2009
    ..Research that increases our understanding of the evolutionary forces that shape patterns of human genetic variation will facilitate disease gene mapping studies. ..
  8. Genome-Wide Analysis of Adaptive Evolution in Humans
    Joshua Akey; Fiscal Year: 2006
    ..Research that increases our understanding of the evolutionary forces that shape patterns of human genetic variation will facilitate disease gene mapping studies. ..