David A Ray

Summary

Affiliation: Mississippi State University
Country: USA

Publications

  1. pmc Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among vesper bats
    Heidi J T Pagan
    Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS, USA
    Genome Biol Evol 4:575-85. 2012
  2. pmc PiggyBac-ing on a primate genome: novel elements, recent activity and horizontal transfer
    Heidi J T Pagan
    Department of Biology, West Virginia University, USA
    Genome Biol Evol 2:293-303. 2010
  3. pmc Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes
    John A St John
    Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
    Genome Biol 13:415. 2012
  4. pmc Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes
    Todd A Castoe
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, 12801 17th Ave, Aurora, CO 80045, USA
    Genome Biol 12:406. 2011
  5. pmc Reading between the LINEs to see into the past
    David A Ray
    Department of Biochemistry and Molecular Biology, Box 9650, Mississippi State University, Mississippi State, MS 39762, USA
    Trends Genet 25:475-9. 2009
  6. pmc Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus
    David A Ray
    Department of Biology, West Virginia University, Morgantown, West Virginia 26506, USA
    Genome Res 18:717-28. 2008
  7. pmc Laboratory methods for the analysis of primate mobile elements
    David A Ray
    Department of Biology, West Virginia University, Morgantown, WV, USA
    Methods Mol Biol 628:153-79. 2010
  8. doi request reprint Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera
    P R Meganathan
    Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
    Gene 492:121-9. 2012
  9. pmc Reading TE leaves: new approaches to the identification of transposable element insertions
    David A Ray
    Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi State, Mississippi 39762, USA
    Genome Res 21:813-20. 2011
  10. ncbi request reprint Multiple chicken repeat 1 lineages in the genomes of oestroid flies
    Michelle L Thompson
    Department of Biology, West Virginia University, Morgantown, WV 26506, USA
    Gene 448:40-5. 2009

Collaborators

Detail Information

Publications18

  1. pmc Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among vesper bats
    Heidi J T Pagan
    Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS, USA
    Genome Biol Evol 4:575-85. 2012
    ..These analyses present the first cohesive description of TE evolution across closely related mammalian species, revealing genome-scale differences in TE content within a single family...
  2. pmc PiggyBac-ing on a primate genome: novel elements, recent activity and horizontal transfer
    Heidi J T Pagan
    Department of Biology, West Virginia University, USA
    Genome Biol Evol 2:293-303. 2010
    ..These findings indicate a more complex history of transposon activity in mammals rather than a uniform shutdown of Class II transposition, which had been suggested by analyses of more common model organisms...
  3. pmc Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes
    John A St John
    Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
    Genome Biol 13:415. 2012
    ..The status of these projects and our planned analyses are described...
  4. pmc Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes
    Todd A Castoe
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, 12801 17th Ave, Aurora, CO 80045, USA
    Genome Biol 12:406. 2011
    ..Here, we describe how this will be done, what analyses this work will include, and provide a timeline...
  5. pmc Reading between the LINEs to see into the past
    David A Ray
    Department of Biochemistry and Molecular Biology, Box 9650, Mississippi State University, Mississippi State, MS 39762, USA
    Trends Genet 25:475-9. 2009
    ..Strategies based on this work might also revolutionize investigations of the interface between TE dynamics and genome diversity...
  6. pmc Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus
    David A Ray
    Department of Biology, West Virginia University, Morgantown, West Virginia 26506, USA
    Genome Res 18:717-28. 2008
    ....
  7. pmc Laboratory methods for the analysis of primate mobile elements
    David A Ray
    Department of Biology, West Virginia University, Morgantown, WV, USA
    Methods Mol Biol 628:153-79. 2010
    ..The number of methods to accomplish these ends is ever growing. Here, we present several protocols designed to assay mobile element-based variation within and among individual genomes...
  8. doi request reprint Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera
    P R Meganathan
    Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
    Gene 492:121-9. 2012
    ..These patterns suggest that mutational and selection forces are acting to different extents within Chiroptera and shape their mitochondrial genomes...
  9. pmc Reading TE leaves: new approaches to the identification of transposable element insertions
    David A Ray
    Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi State, Mississippi 39762, USA
    Genome Res 21:813-20. 2011
    ..Herein, we explore the methods reported in the manuscripts and discuss their applications to aspects of human biology and the biology of other organisms...
  10. ncbi request reprint Multiple chicken repeat 1 lineages in the genomes of oestroid flies
    Michelle L Thompson
    Department of Biology, West Virginia University, Morgantown, WV 26506, USA
    Gene 448:40-5. 2009
    ..This work will serve as the basis for additional analyses targeted at developing a simple, efficient marker system for the identification of forensically important carrion flies...
  11. ncbi request reprint Bats with hATs: evidence for recent DNA transposon activity in genus Myotis
    David A Ray
    Department of Biology, West Virginia University, USA
    Mol Biol Evol 24:632-9. 2007
    ..Furthermore, the identification of a likely autonomous element may lead to new approaches for mammalian genetic manipulation...
  12. doi request reprint A non-LTR retroelement extinction in Spermophilus tridecemlineatus
    Roy N Platt
    Department of Biochemistry, Mississippi State University, Mississippi State, MS 39762, USA
    Gene 500:47-53. 2012
    ..Such a finding represents only the fourth instance of a loss of non-LTR retrotransposon activity identified in mammals and, as such, represents an important additional data point to guide our understanding of LINE dynamics in eutherians...
  13. pmc The evolution and diversity of DNA transposons in the genome of the Lizard Anolis carolinensis
    Peter A Novick
    Department of Biology, Queens College, The City University of New York, NY, USA
    Genome Biol Evol 3:1-14. 2011
    ..We propose that the scarcity of old copies in the anole genome results from the rapid decay of elements, caused by a high rate of DNA loss...
  14. pmc Transcriptome-based differentiation of closely-related Miscanthus lines
    Philippe Chouvarine
    Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
    PLoS ONE 7:e29850. 2012
    ..We provide the first exome sequence database for Miscanthus species complete with Gene Ontology (GO) functional annotations...
  15. ncbi request reprint SINEs of a nearly perfect character
    David A Ray
    Department of Biology, West Virginia University, PO Box 6057, Morgantown, West Virginia 26506, USA
    Syst Biol 55:928-35. 2006
    ....
  16. ncbi request reprint SINEs of progress: Mobile element applications to molecular ecology
    David A Ray
    Department of Biology, West Virginia University, 53 Campus Dr, Morgantown, WV 26506, USA
    Mol Ecol 16:19-33. 2007
    ..In this review, I discuss the application of mobile element markers, especially short interspersed elements (SINEs), to phylogenetic and population data, with an emphasis on potential applications to molecular ecology...
  17. pmc A bacterial artificial chromosome library for the Australian saltwater crocodile (Crocodylus porosus) and its utilization in gene isolation and genome characterization
    Xueyan Shan
    Mississippi Genome Exploration Laboratory, Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, USA
    BMC Genomics 10:S9. 2009
    ..This is the first BAC library for a crocodile and only the second BAC resource for a crocodilian...
  18. ncbi request reprint Large numbers of novel miRNAs originate from DNA transposons and are coincident with a large species radiation in bats
    Roy N Platt
    Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityInstitute for Genomics, Biocomputing and Biotechnology, Mississippi State University
    Mol Biol Evol 31:1536-45. 2014
    ..Our observations suggest a mechanism for introducing functional genomic variation rapidly through the expansion of DNA transposons that fits within the TE-thrust hypothesis. ..