Eric A Stone

Summary

Affiliation: North Carolina State University
Country: USA

Publications

  1. pmc Identification of RNA binding motif proteins essential for cardiovascular development
    Samantha Maragh
    Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
    BMC Dev Biol 11:62. 2011
  2. pmc Joint genotyping on the fly: identifying variation among a sequenced panel of inbred lines
    Eric A Stone
    Department of Genetics and Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27603, USA
    Genome Res 22:966-74. 2012
  3. pmc Constructing a meaningful evolutionary average at the phylogenetic center of mass
    Eric A Stone
    Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695 7566, USA
    BMC Bioinformatics 8:222. 2007
  4. pmc Modulated modularity clustering as an exploratory tool for functional genomic inference
    Eric A Stone
    Department of Statistics, North Carolina State University, Raleigh, NC, USA
    PLoS Genet 5:e1000479. 2009
  5. pmc Alcohol sensitivity in Drosophila: translational potential of systems genetics
    Tatiana V Morozova
    Department of Biology, W M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695, USA
    Genetics 183:733-45, 1SI-12SI. 2009
  6. pmc A transcriptional network associated with natural variation in Drosophila aggressive behavior
    Alexis C Edwards
    Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
    Genome Biol 10:R76. 2009
  7. pmc Plasticity of the chemoreceptor repertoire in Drosophila melanogaster
    Shanshan Zhou
    Department of Biology, North Carolina State University, Raleigh, North Carolina, United States of America
    PLoS Genet 5:e1000681. 2009
  8. pmc Systems genetics of complex traits in Drosophila melanogaster
    Julien F Ayroles
    Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
    Nat Genet 41:299-307. 2009
  9. pmc Epistasis dominates the genetic architecture of Drosophila quantitative traits
    Wen Huang
    Department of Genetics, North Carolina State University, Raleigh, NC 27695, USA
    Proc Natl Acad Sci U S A 109:15553-9. 2012
  10. pmc Phenotypic plasticity of the Drosophila transcriptome
    Shanshan Zhou
    Department of Biology, North Carolina State University, Raleigh, North Carolina, United States of America
    PLoS Genet 8:e1002593. 2012

Detail Information

Publications32

  1. pmc Identification of RNA binding motif proteins essential for cardiovascular development
    Samantha Maragh
    Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
    BMC Dev Biol 11:62. 2011
    ....
  2. pmc Joint genotyping on the fly: identifying variation among a sequenced panel of inbred lines
    Eric A Stone
    Department of Genetics and Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27603, USA
    Genome Res 22:966-74. 2012
    ..In doing so, we illustrate how JGIL is robust to moderate levels of error. Supported by these analyses, we advocate the importance of modeling the data and the experimental design when possible...
  3. pmc Constructing a meaningful evolutionary average at the phylogenetic center of mass
    Eric A Stone
    Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695 7566, USA
    BMC Bioinformatics 8:222. 2007
    ..Here we propose a remedy that weighs the contribution of each species according to its phylogenetic placement...
  4. pmc Modulated modularity clustering as an exploratory tool for functional genomic inference
    Eric A Stone
    Department of Statistics, North Carolina State University, Raleigh, NC, USA
    PLoS Genet 5:e1000479. 2009
    ..We show MMC to be effective and suitable to applications of large scale. In light of these features, we advocate MMC as a standard tool for exploration and hypothesis generation...
  5. pmc Alcohol sensitivity in Drosophila: translational potential of systems genetics
    Tatiana V Morozova
    Department of Biology, W M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695, USA
    Genetics 183:733-45, 1SI-12SI. 2009
    ....
  6. pmc A transcriptional network associated with natural variation in Drosophila aggressive behavior
    Alexis C Edwards
    Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
    Genome Biol 10:R76. 2009
    ..Populations of Drosophila melanogaster harbor quantitative genetic variation in aggressive behavior, providing an excellent model system for dissecting the genetic basis of naturally occurring variation in aggression...
  7. pmc Plasticity of the chemoreceptor repertoire in Drosophila melanogaster
    Shanshan Zhou
    Department of Biology, North Carolina State University, Raleigh, North Carolina, United States of America
    PLoS Genet 5:e1000681. 2009
    ..This finely pixilated modular organization of the chemosensory subgenome enables fine tuning of the expression of the chemoreceptor repertoire in response to ecologically relevant environmental and physiological conditions...
  8. pmc Systems genetics of complex traits in Drosophila melanogaster
    Julien F Ayroles
    Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
    Nat Genet 41:299-307. 2009
    ..Overlapping transcripts in modules associated with different traits provide insight into the molecular basis of pleiotropy between complex traits...
  9. pmc Epistasis dominates the genetic architecture of Drosophila quantitative traits
    Wen Huang
    Department of Genetics, North Carolina State University, Raleigh, NC 27695, USA
    Proc Natl Acad Sci U S A 109:15553-9. 2012
    ..Knowledge of epistatic networks will contribute to our understanding of the genetic basis of evolutionarily and clinically important traits and enhance predictive ability at an individualized level in medicine and agriculture...
  10. pmc Phenotypic plasticity of the Drosophila transcriptome
    Shanshan Zhou
    Department of Biology, North Carolina State University, Raleigh, North Carolina, United States of America
    PLoS Genet 8:e1002593. 2012
    ..Our analysis suggests that a restricted environmentally responsive segment of the transcriptome preserves the balance between phenotypic plasticity and environmental canalization...
  11. pmc Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks
    Julien F Ayroles
    Department of Genetics, North Carolina State University, Raleigh, NC 27695, USA
    Genet Res (Camb) 93:387-95. 2011
    ..We argue that this method can be extended to other systems for which information on genetic variation in gene expression is available...
  12. pmc The Drosophila melanogaster Genetic Reference Panel
    Trudy F C Mackay
    Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
    Nature 482:173-8. 2012
    ..Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics...
  13. pmc The effects of weak genetic perturbations on the transcriptome of the wing imaginal disc and its association with wing shape in Drosophila melanogaster
    Ian Dworkin
    Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
    Genetics 187:1171-84. 2011
    ..We discuss these results in the light of possible attractor states of gene expression and how this would affect interpretation of covariation between transcriptional profiles and other phenotypes...
  14. ncbi request reprint Trade-offs in detecting evolutionarily constrained sequence by comparative genomics
    Eric A Stone
    Department of Statistics, Stanford University, Stanford, California 94305, USA
    Annu Rev Genomics Hum Genet 6:143-64. 2005
    ..We consider the impact of an expanding diversity of orthologous sequences on our ability to resolve functional elements. This impact is assessed through both recent comparative analyses of deep alignments and mathematical modeling...
  15. pmc The non-random clustering of non-synonymous substitutions and its relationship to evolutionary rate
    Lisa G McFerrin
    Graduate Program in Bioinformatics, North Carolina State University, Raleigh, NC 27695 7566, USA
    BMC Genomics 12:415. 2011
    ..We invert this paradigm by leveraging the regional nature of protein structure and function to both illuminate and make use of genome-wide patterns of local sequence conservation...
  16. doi request reprint The genetics of quantitative traits: challenges and prospects
    Trudy F C Mackay
    Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
    Nat Rev Genet 10:565-77. 2009
    ..This systems genetics approach enables us to understand the biology inside the 'black box' that lies between genotype and phenotype in terms of causal networks of interacting genes...
  17. pmc Fine-scale heterogeneity in crossover rate in the garnet-scalloped region of the Drosophila melanogaster X chromosome
    Nadia D Singh
    Department of Genetics, North Carolina State University, Raleigh, NC 27695, USA
    Genetics 194:375-87. 2013
    ..Our results shed new light on the scale and magnitude of crossover rate heterogeneity in D. melanogaster and highlight potential features mediating this heterogeneity...
  18. pmc Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity
    Eric A Stone
    Department of Statistics, Stanford University, Stanford, California 94305 5324, USA
    Genome Res 15:978-86. 2005
    ....
  19. pmc Why the phylogenetic regression appears robust to tree misspecification
    Eric A Stone
    Department of Genetics, North Carolina State University, Raleigh, NC 27695 8203, USA eric
    Syst Biol 60:245-60. 2011
    ..I discuss why soft polytomies do not meet these problematic conditions, leading to the conclusion that unresolved bifurcations should have only modest effects on the regression fit...
  20. pmc Mixture modeling of transcript abundance classes in natural populations
    Wen Ping Hsieh
    Department of Genetics, Gardner Hall, North Carolina State University, Raleigh, North Carolina 27695 7614, USA
    Genome Biol 8:R98. 2007
    ..Here, we explore the distributions of cis-acting and trans-acting factors and their relative contributions to expression of transcripts that exhibit two or more classes of abundance among individuals within populations...
  21. pmc Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees
    Sarah D Kocher
    Department of Genetics, North Carolina State University, Raleigh, North Carolina, United States of America
    PLoS ONE 5:e9116. 2010
    ..In honey bees, the reproductive queen produces a pheromonal signal that regulates many aspects of worker behavior and physiology and maintains colony organization...
  22. pmc Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
    Wen Huang
    Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA
    Genome Res 24:1193-208. 2014
    ..The DGRP lines, sequence data, genotypes, quality scores, phenotypes, and analysis and visualization tools are publicly available. ..
  23. pmc Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci
    Sang Chul Choi
    Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695 7566, USA
    Gene 441:45-52. 2009
    ..We find that our technique for employing protein tertiary structure information yields some biologically plausible results but that it does not substantially improve the inference of ancestral human allele types...
  24. pmc Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep
    Susan T Harbison
    Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
    Nat Genet 41:371-5. 2009
    ..We confirmed co-regulated gene expression using P-element mutants. Quantitative genetic analysis of natural phenotypic variation is an efficient method for revealing candidate genes and pathways...
  25. doi request reprint Effect of sexual recombination on population diversity in aflatoxin production by Aspergillus flavus and evidence for cryptic heterokaryosis
    Rodrigo A Olarte
    Department of Plant Pathology, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA
    Mol Ecol 21:1453-76. 2012
    ..flavus. The results of this study have significant implications for managing AF contamination of crops and for improving biocontrol strategies using nonaflatoxigenic strains of A. flavus...
  26. ncbi request reprint Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Richard A Gibbs
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA lt http www hgsc bcm tmc edu
    Nature 428:493-521. 2004
    ....
  27. pmc Characterization of evolutionary rates and constraints in three Mammalian genomes
    Gregory M Cooper
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genome Res 14:539-48. 2004
    ..At least 5% of the human genome is under substantial constraint, most of which is noncoding...
  28. pmc Phenotype-genotype correlation in Hirschsprung disease is illuminated by comparative analysis of the RET protein sequence
    Carl S Kashuk
    McKusick Nathans Institute of Genetic Medicine and Department of Comparative Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Proc Natl Acad Sci U S A 102:8949-54. 2005
    ....
  29. pmc Distribution and intensity of constraint in mammalian genomic sequence
    Gregory M Cooper
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genome Res 15:901-13. 2005
    ..We anticipate that GERP and the types of analyses it facilitates will provide further insights and improved annotation for the human genome as mammalian genome sequence data become richer...
  30. pmc Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
    Elliott H Margulies
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Res 17:760-74. 2007
    ..Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization...
  31. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  32. pmc Inference of functional regions in proteins by quantification of evolutionary constraints
    Alexander L Simon
    Program in Cancer Biology and Department of Pathology, Stanford University Medical School, Stanford, CA 94305 5324, USA
    Proc Natl Acad Sci U S A 99:2912-7. 2002
    ..The methodology has significant predictive power and may be used to guide structure--function studies for any protein represented by a modest number of homologs in sequence databases...