David A Ray
Affiliation: Mississippi State University
- Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among vesper batsHeidi 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...
- PiggyBac-ing on a primate genome: novel elements, recent activity and horizontal transferHeidi 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...
- Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotesJohn 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...
- Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakesTodd 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...
- Reading between the LINEs to see into the pastDavid 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...
- Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugusDavid A Ray
Department of Biology, West Virginia University, Morgantown, West Virginia 26506, USA
Genome Res 18:717-28. 2008....
- Laboratory methods for the analysis of primate mobile elementsDavid 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...
- 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 ChiropteraP 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...
- Reading TE leaves: new approaches to the identification of transposable element insertionsDavid 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...
- Multiple chicken repeat 1 lineages in the genomes of oestroid fliesMichelle 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...
- Bats with hATs: evidence for recent DNA transposon activity in genus MyotisDavid 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...
- A non-LTR retroelement extinction in Spermophilus tridecemlineatusRoy 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...
- The evolution and diversity of DNA transposons in the genome of the Lizard Anolis carolinensisPeter 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...
- Transcriptome-based differentiation of closely-related Miscanthus linesPhilippe 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...
- SINEs of a nearly perfect characterDavid A Ray
Department of Biology, West Virginia University, PO Box 6057, Morgantown, West Virginia 26506, USA
Syst Biol 55:928-35. 2006....
- SINEs of progress: Mobile element applications to molecular ecologyDavid 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...
- A bacterial artificial chromosome library for the Australian saltwater crocodile (Crocodylus porosus) and its utilization in gene isolation and genome characterizationXueyan 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...
- Large numbers of novel miRNAs originate from DNA transposons and are coincident with a large species radiation in batsRoy 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. ..