Mark A Batzer

Summary

Affiliation: Louisiana State University
Country: USA

Publications

  1. ncbi Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers
    Jerilyn A Walker
    Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Mob DNA 3:8. 2012
  2. ncbi Mobile element scanning (ME-Scan) by targeted high-throughput sequencing
    David J Witherspoon
    Dept of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
    BMC Genomics 11:410. 2010
  3. ncbi Alu repeats increase local recombination rates
    David J Witherspoon
    Dept of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
    BMC Genomics 10:530. 2009
  4. ncbi Nuclear versus mitochondrial DNA: evidence for hybridization in colobine monkeys
    Christian Roos
    Primate Genetics Laboratory, German Primate Center, Gottingen, Germany
    BMC Evol Biol 11:77. 2011
  5. ncbi Heads or tails: L1 insertion-associated 5' homopolymeric sequences
    Thomas J Meyer
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Bldg, Baton Rouge, LA 70803, USA
    Mob DNA 1:7. 2010
  6. ncbi Alu repeats and human genomic diversity
    Mark A Batzer
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
    Nat Rev Genet 3:370-9. 2002
  7. ncbi Alu pair exclusions in the human genome
    George W Cook
    Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
    Mob DNA 2:10. 2011
  8. ncbi Allele frequencies of the human platelet antigen-1 in the Egyptian population
    Abdel Halim Salem
    Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
    BMC Res Notes 2:90. 2009
  9. ncbi High frequency of the D allele of the angiotensin-converting enzyme gene in Arabic populations
    Abdel Halim Salem
    Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA
    BMC Res Notes 2:99. 2009
  10. ncbi Under the genomic radar: the stealth model of Alu amplification
    Kyudong Han
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA
    Genome Res 15:655-64. 2005

Detail Information

Publications86

  1. ncbi Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers
    Jerilyn A Walker
    Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Mob DNA 3:8. 2012
    ..abstract:..
  2. ncbi Mobile element scanning (ME-Scan) by targeted high-throughput sequencing
    David J Witherspoon
    Dept of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
    BMC Genomics 11:410. 2010
    ....
  3. ncbi Alu repeats increase local recombination rates
    David J Witherspoon
    Dept of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
    BMC Genomics 10:530. 2009
    ....
  4. ncbi Nuclear versus mitochondrial DNA: evidence for hybridization in colobine monkeys
    Christian Roos
    Primate Genetics Laboratory, German Primate Center, Gottingen, Germany
    BMC Evol Biol 11:77. 2011
    ....
  5. ncbi Heads or tails: L1 insertion-associated 5' homopolymeric sequences
    Thomas J Meyer
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Bldg, Baton Rouge, LA 70803, USA
    Mob DNA 1:7. 2010
    ..Twin priming, a variant of TPRT, can result in unusual DNA sequence architecture. These insertions appear to be inverted, truncated L1s flanked by target site duplications...
  6. ncbi Alu repeats and human genomic diversity
    Mark A Batzer
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
    Nat Rev Genet 3:370-9. 2002
    ..Alu-insertion polymorphisms are a boon for the study of human population genetics and primate comparative genomics because they are neutral genetic markers of identical descent with known ancestral states...
  7. ncbi Alu pair exclusions in the human genome
    George W Cook
    Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
    Mob DNA 2:10. 2011
    ..abstract:..
  8. ncbi Allele frequencies of the human platelet antigen-1 in the Egyptian population
    Abdel Halim Salem
    Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
    BMC Res Notes 2:90. 2009
    ..This study is the first to investigate the allele frequency of the HPA-1 system in the Egyptian population and serves as an outline for future clinical research associated with platelet disorders in this group...
  9. ncbi High frequency of the D allele of the angiotensin-converting enzyme gene in Arabic populations
    Abdel Halim Salem
    Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA
    BMC Res Notes 2:99. 2009
    ....
  10. ncbi Under the genomic radar: the stealth model of Alu amplification
    Kyudong Han
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA
    Genome Res 15:655-64. 2005
    ....
  11. ncbi Tracking Alu evolution in New World primates
    David A Ray
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio Modular Multiscale Systems, Louisiana State University, Baton Rouge, LA 70803, USA
    BMC Evol Biol 5:51. 2005
    ....
  12. ncbi Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages
    Kyudong Han
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Nucleic Acids Res 33:4040-52. 2005
    ..In addition, we show that internal rearrangements can modify L1 structure during retrotransposition events associated with large deletions...
  13. ncbi Alu recombination-mediated structural deletions in the chimpanzee genome
    Kyudong Han
    Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
    PLoS Genet 3:1939-49. 2007
    ....
  14. ncbi Analysis of the human Alu Ye lineage
    Abdel Halim Salem
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio Modular Multi Scale Systems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
    BMC Evol Biol 5:18. 2005
    ..Alu elements are therefore a rich source of inter- and intra-species primate genomic variation...
  15. ncbi Following the LINEs: an analysis of primate genomic variation at human-specific LINE-1 insertion sites
    Bethaney J Vincent
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, USA
    Mol Biol Evol 20:1338-48. 2003
    ..Therefore, L1 insertion polymorphisms appear to be essentially homoplasy free characters well suited for the study of population genetics and phylogenetic relationships within closely related species...
  16. ncbi Recently integrated Alu elements and human genomic diversity
    Abdel-Halim Salem
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, USA
    Mol Biol Evol 20:1349-61. 2003
    ..This type of Alu retroposition-mediated genomic deletion is a novel source of lineage-specific evolution within primate genomes...
  17. ncbi Human genomic deletions mediated by recombination between Alu elements
    Shurjo K Sen
    Department of Biological Sciences, Louisiana State University, Baton Rouge, 70803, USA
    Am J Hum Genet 79:41-53. 2006
    ..Overall, we found that Alu recombination-mediated genomic deletion has had a much higher impact than was inferred from previously identified isolated events and that it continues to contribute to the dynamic nature of the human genome...
  18. ncbi Emergence of primate genes by retrotransposon-mediated sequence transduction
    Jinchuan Xing
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA
    Proc Natl Acad Sci U S A 103:17608-13. 2006
    ..The duplication of entire genes and the creation of previously undescribed gene families through retrotransposon-mediated sequence transduction represent an important mechanism by which mobile elements impact their host genomes...
  19. ncbi Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome
    Kyudong Han
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio Modular Multi Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA
    Science 316:238-40. 2007
    ..Mobile elements compose roughly 50% of primate genomes, and our findings illustrate their diversity and strong influence on genome evolution between closely related species...
  20. ncbi Genome-wide analysis of the human Alu Yb-lineage
    Anthony B Carter
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Hum Genomics 1:167-78. 2004
    ..The high copy number, level of insertion polymorphism and estimated age indicate that members of the Alu Yb elements will be useful in a wide range of genetic analyses...
  21. ncbi Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons
    Jungnam Lee
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi Scale Systems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Gene 390:18-27. 2007
    ..Therefore, the chimpanzee genome constitutes an excellent model in which to analyze the evolutionary dynamics of L1 retrotransposons...
  22. ncbi Analysis of the human Alu Ya-lineage
    Anthony C Otieno
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Microsystems, Louisiana State University, 202 Life Sciences Building, Baton Rouge 70803, USA
    J Mol Biol 342:109-18. 2004
    ..The size, evolutionary age and variable allele insertion frequencies of several of these subfamilies makes members of the Ya-lineage useful tools for human population studies and primate phylogenetics...
  23. ncbi Comprehensive analysis of Alu-associated diversity on the human sex chromosomes
    Pauline A Callinan
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Gene 317:103-10. 2003
    ..The Alu insertion polymorphisms identified in this study should prove useful for the study of human population genetics...
  24. ncbi Mobile element-based forensic genomics
    David A Ray
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Mutat Res 616:24-33. 2007
    ..These tools include quantitative species-specific DNA detection, analysis of complex biomaterials, and the inference of geographic origin of human DNA samples...
  25. ncbi Differential alu mobilization and polymorphism among the human and chimpanzee lineages
    Dale J Hedges
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, Louisiana 70803, USA
    Genome Res 14:1068-75. 2004
    ..We propose a population-based model to account for the observed fluctuation in Alu retroposition rates across primate taxa...
  26. ncbi Alu insertion loci and platyrrhine primate phylogeny
    David A Ray
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Multi-Scale Systems, Louisiana State University, 202 Life Sciences Bldg, Baton Rouge, LA 70803, USA
    Mol Phylogenet Evol 35:117-26. 2005
    ..00. In this study, we report one of the largest applications of SINE elements to phylogenetic analysis to date, and the results provide a robust molecular phylogeny for platyrrhine primates...
  27. ncbi A mobile element based phylogeny of Old World monkeys
    Jinchuan Xing
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Multi-Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA
    Mol Phylogenet Evol 37:872-80. 2005
    ..Relationships among all major clades are in general agreement with other molecular and morphological data sets but have stronger statistical support...
  28. ncbi Internal priming: an opportunistic pathway for L1 and Alu retrotransposition in hominins
    Deepa Srikanta
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Gene 448:233-41. 2009
    ..Also, we demonstrate that the internal priming process is associated with inter-chromosomal duplications and the insertion of filler DNA...
  29. ncbi An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair
    Deepa Srikanta
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA
    Genomics 93:205-12. 2009
    ....
  30. ncbi From the margins of the genome: mobile elements shape primate evolution
    Dale J Hedges
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, LA 70803, USA
    Bioessays 27:785-94. 2005
    ..Here we review advances in our understanding of the host-mobile element dynamic and its overall impact on primate evolution...
  31. ncbi Chromosomal inversions between human and chimpanzee lineages caused by retrotransposons
    Jungnam Lee
    Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
    PLoS ONE 3:e4047. 2008
    ..This study is the first comprehensive analysis of mobile element bases inversion breakpoints between human and chimpanzee lineages, and highlights their role in primate genome evolution...
  32. ncbi L1 recombination-associated deletions generate human genomic variation
    Kyudong Han
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA
    Proc Natl Acad Sci U S A 105:19366-71. 2008
    ..Overall, there is increasing evidence that L1RADs have played an important role in creating structural variation...
  33. ncbi Alu elements and hominid phylogenetics
    Abdel-Halim Salem
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Proc Natl Acad Sci U S A 100:12787-91. 2003
    ..Here we present the strongest evidence reported to date for a sister relationship between humans and chimpanzees while clearly distinguishing the chimpanzee and human lineages...
  34. ncbi Comprehensive analysis of two Alu Yd subfamilies
    Jinchuan Xing
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    J Mol Evol 57:S76-89. 2003
    ..These Alu subfamilies are a source of genomic fossil relics for the study of primate phylogenetics and human population genetics...
  35. ncbi LINE-1 preTa elements in the human genome
    Abdel Halim Salem
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    J Mol Biol 326:1127-46. 2003
    ..In all, 29 have two intact open reading frames and may be capable of retrotransposition...
  36. ncbi Modeling the amplification dynamics of human Alu retrotransposons
    Dale J Hedges
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Microsystems, Louisiana State University, Baton Rouge, Louisiana, United States of America
    PLoS Comput Biol 1:e44. 2005
    ....
  37. ncbi Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome
    Shurjo K Sen
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA
    Nucleic Acids Res 35:3741-51. 2007
    ..We show that endonuclease-independent L1 insertions are structurally distinguishable from classical L1 insertion loci, and that they are associated with inter-chromosomal translocations and deletions of target genomic DNA...
  38. ncbi Straightening out the LINEs: LINE-1 orthologous loci
    Huei Jin Ho
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Genomics 85:201-7. 2005
    ..Sequence analysis showed that both elements were clearly distinguishable from their human counterparts. We conclude that L1 elements can continue to be regarded as essentially homoplasy-free genetic characters...
  39. ncbi Quantitative PCR for DNA identification based on genome-specific interspersed repetitive elements
    Jerilyn A Walker
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Genomics 83:518-27. 2004
    ..The 10 assays reported here will help facilitate the sensitive detection and quantitation of common domestic animal and bird species DNA from complex biomaterials...
  40. ncbi Human DNA quantitation using Alu element-based polymerase chain reaction
    Jerilyn A Walker
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA
    Anal Biochem 315:122-8. 2003
    ..The introduction of these assays to forensic laboratories will undoubtedly increase the sensitivity and specificity of human DNA detection and quantitation from complex sources...
  41. ncbi SVA elements: a hominid-specific retroposon family
    Hui Wang
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    J Mol Biol 354:994-1007. 2005
    ..This makes SVA elements the youngest family of retroposons in the primate order...
  42. ncbi A mobile element-based evolutionary history of guenons (tribe Cercopithecini)
    Jinchuan Xing
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio Modular Multi Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA
    BMC Biol 5:5. 2007
    ..SINEs are a class of non-autonomous mobile elements and are essentially homoplasy-free characters with known ancestral states, making them useful genetic markers for phylogenetic studies...
  43. ncbi Multiplex polymerase chain reaction for simultaneous quantitation of human nuclear, mitochondrial, and male Y-chromosome DNA: application in human identification
    Jerilyn A Walker
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Microsystems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Anal Biochem 337:89-97. 2005
    ..Mainstream application of these assays will undoubtedly benefit forensic genomics...
  44. ncbi Resolution of mixed human DNA samples using mitochondrial DNA sequence variants
    Jerilyn A Walker
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Anal Biochem 325:171-3. 2004
  45. ncbi Recently integrated Alu retrotransposons are essentially neutral residents of the human genome
    Richard Cordaux
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Gene 373:138-44. 2006
    ..These results also imply that selective processes specifically targeting Alu elements can be ruled out as explanations for the accumulation of Alu elements in GC-rich regions of the human genome...
  46. ncbi Estimating the retrotransposition rate of human Alu elements
    Richard Cordaux
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Gene 373:134-7. 2006
    ..These results suggest that Alu elements retrotranspose at a faster rate in humans than previously thought, and support the potential of Alu elements as mutagenic factors in the human genome...
  47. ncbi Phylogeny of the macaques (Cercopithecidae: Macaca) based on Alu elements
    Jing Li
    Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
    Gene 448:242-9. 2009
    ....
  48. ncbi A SINE-based dichotomous key for primate identification
    Scott W Herke
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio Modular Microsystems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, United States
    Gene 390:39-51. 2007
    ..With newly emerging genome databases, finding informative retrotransposon insertions is becoming much more rapid; thus, the general principle of using SINEs to identify organisms is broadly applicable...
  49. ncbi Teaching an old dog new tricks: SINEs of canine genomic diversity
    Richard Cordaux
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Proc Natl Acad Sci U S A 103:1157-8. 2006
  50. ncbi Alu retrotransposition-mediated deletion
    Pauline A Callinan
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    J Mol Biol 348:791-800. 2005
    ..A comprehensive analysis of the collateral effects by Alu mobilization on all primate genomes will require sequenced genomes from representatives of the entire order...
  51. ncbi Birth of a chimeric primate gene by capture of the transposase gene from a mobile element
    Richard Cordaux
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi Scale Systems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Proc Natl Acad Sci U S A 103:8101-6. 2006
    ..Our results not only provide insight into the conditions required for a successful gene fusion, but they also suggest a mechanism by which the circuitry underlying complex regulatory networks may be rapidly established...
  52. ncbi Inference of human geographic origins using Alu insertion polymorphisms
    David A Ray
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Forensic Sci Int 153:117-24. 2005
    ..This technique to infer the geographic affiliation of unknown human DNA samples will be a useful tool in forensic genomics...
  53. ncbi Chompy: an infestation of MITE-like repetitive elements in the crocodilian genome
    David A Ray
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Multiscale Systems, Louisiana State University, 202 Life Sciences Bldg, Baton Rouge, LA 70803, USA
    Gene 362:1-10. 2005
    ..As a result of their size and unique properties, Chompy elements may provide a useful source of genomic variation for crocodilian comparative genomics...
  54. ncbi Distribution of the HIV resistance CCR5-Delta32 allele among Egyptians and Syrians
    Abdel Halim Salem
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio Modular Multiscale Systems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Mutat Res 616:175-80. 2007
    ..The presence of the CCR5-Delta32 allele among Egyptians may be attributed to the admixture with people of European descent. Thus we conclude that the protective deletion CCR5-Delta32 is largely absent in the Egyptian population...
  55. ncbi Retrotransposition of Alu elements: how many sources?
    Richard Cordaux
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA
    Trends Genet 20:464-7. 2004
    ..This multiplicity of source elements provides new insight into the remarkably successful amplification strategy of the Alu family...
  56. ncbi Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies
    Miriam K Konkel
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi Scale Systems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Gene 390:28-38. 2007
    ..Our results also suggest that the exhaustive identification of L1 insertion polymorphisms is far from complete, and new whole genome sequences are valuable sources for finding novel retrotransposon insertion polymorphisms...
  57. ncbi An Alu-based phylogeny of gibbons (hylobatidae)
    Thomas J Meyer
    Department of Biological Sciences, Louisiana State University
    Mol Biol Evol 29:3441-50. 2012
    ..Our findings will aid in the conservation of these threatened primates and inform future studies of the biogeographical history and distribution of modern gibbon species...
  58. ncbi Quantitative intra-short interspersed element PCR for species-specific DNA identification
    Jerilyn A Walker
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge 70803, USA
    Anal Biochem 316:259-69. 2003
    ..The SINE-based PCR methods we report here are species-specific, are highly sensitive, and will improve the detection limits for DNA sequences derived from these species...
  59. ncbi In search of polymorphic Alu insertions with restricted geographic distributions
    Richard Cordaux
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA
    Genomics 90:154-8. 2007
    ..This is desirable if Alu insertion polymorphisms are to be used for human evolution studies or forensic applications...
  60. ncbi An alu-based phylogeny of lemurs (infraorder: Lemuriformes)
    Adam T McLain
    Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
    PLoS ONE 7:e44035. 2012
    ..Our results also support the monophyly of the Lemuridae. Within Lemuridae we place Lemur and Hapalemur together to the exclusion of Eulemur and Varecia, with Varecia the sister lineage to the other three genera...
  61. ncbi Alu element mutation spectra: molecular clocks and the effect of DNA methylation
    Jinchuan Xing
    Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Microsystems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    J Mol Biol 344:675-82. 2004
    ....
  62. ncbi A comprehensive analysis of recently integrated human Ta L1 elements
    Jeremy S Myers
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Am J Hum Genet 71:312-26. 2002
    ..One hundred fifteen (45%) of the Ta L1 elements were polymorphic with respect to insertion presence or absence and will serve as identical-by-descent markers for the study of human evolution...
  63. ncbi A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome
    Miriam K Konkel
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA
    Semin Cancer Biol 20:211-21. 2010
    ..This may be at least partially attributed to the commonly seen global hypomethylation as well as general epigenetic dysfunction of cancer cells. Where possible, we provide examples that impact cancer predisposition and/or development...
  64. ncbi Mobile element-based assay for human gender determination
    Dale J Hedges
    Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
    Anal Biochem 312:77-9. 2003
  65. ncbi Mammalian retroelements
    Prescott L Deininger
    Tulane Cancer Center, Department of Environmental Health Sciences, Tulane University Health Sciences Center, New Orleans, Louisiana 70112, USA
    Genome Res 12:1455-65. 2002
    ....
  66. ncbi Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms
    Jianxin Wang
    Department of Cancer Genetics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
    Gene 365:11-20. 2006
    ..Among chromosomes, the density of Alu insertion polymorphisms is positively correlated with the Alu-site availability and is inversely correlated with the densities of older Alu elements and genes...
  67. ncbi Human population genetic structure and inference of group membership
    Michael J Bamshad
    Department of Pediatrics, University of Utah, Salt Lake City, Utah 84112, USA
    Am J Hum Genet 72:578-89. 2003
    ..This suggests that a more flexible framework is needed for making inferences about population structure and the utility of proxies...
  68. ncbi Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms
    W Scott Watkins
    Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
    Genome Res 13:1607-18. 2003
    ..These analyses also demonstrate that markers with higher F(ST) values have greater resolving power and produce more consistent genetic distance estimates...
  69. ncbi Active Alu element "A-tails": size does matter
    Astrid M Roy-Engel
    Tulane Cancer Center, SL-66, Department of Environmental Health Sciences, Tulane University-Health Sciences Center, New Orleans, Louisiana 70112, USA
    Genome Res 12:1333-44. 2002
    ..On the basis of these observations, a model is presented for the role of A-tail length in determining which Alu elements are active...
  70. ncbi Polymorphisms within a polymorphism: SNPs in and around a polymorphic Alu insertion in intron 44 of the human dystrophin gene
    Alan D Lovell
    Centre de Recherche, , , , QC, Canada, H3T 1C5
    J Hum Genet 49:269-72. 2004
    ....
  71. ncbi Non-traditional Alu evolution and primate genomic diversity
    Astrid M Roy-Engel
    Department of Environmental Health Sciences, Tulane Cancer Center SL-66, Tulane University Medical Center, 1430 Tulane Ave, New Orleans, LA 70112, USA
    J Mol Biol 316:1033-40. 2002
    ..This study suggests that the majority of Alu insertions in primate genomes are the products of unique evolutionary events...
  72. ncbi Alu insertion polymorphisms in Native Americans and related Asian populations
    Jaqueline Battilana
    Centro de Biologia Genômica e Molecular, Pontificia Universidade Catolica do Rio Grande do Sul, Faculdade de Biociencias, Porto Alegre, RS, Brazil
    Ann Hum Biol 33:142-60. 2006
    ..Alu insertions provide useful markers for the study of inter-population affinities and historical processes, but data on these systems are not numerous in Native Americans and related populations...
  73. ncbi Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity
    Maria del Carmen Seleme
    Department of Genetics, Division of Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Proc Natl Acad Sci U S A 103:6611-6. 2006
    ..These data suggest that individual variation in retrotransposition potential makes an important contribution to human genetic diversity...
  74. ncbi Ancestral alleles and population origins: inferences depend on mutation rate
    Alan R Rogers
    Department of Anthropology, University of Utah, USA
    Mol Biol Evol 24:990-7. 2007
    ..This is true of one data set, but not of 2 others. This also suggests the action of some factor, such as selection or ascertainment bias, that varies among data sets...
  75. ncbi dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans
    Jianxin Wang
    Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
    Hum Mutat 27:323-9. 2006
    ..dbRIP represents the first database providing comprehensive, integrative, and interactive compilation of RIP data, and it will be a useful resource for researchers working in the area of human genetics...
  76. ncbi SINEs, evolution and genome structure in the opossum
    Wanjun Gu
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
    Gene 396:46-58. 2007
    ..Like eutherians, metatherian (marsupial) mammals have evolved high CpG substitution rates, but this is apparently a convergence in process rather than a shared ancestral state...
  77. ncbi Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica
    Andrew J Gentles
    Department of Radiology, School of Medicine, Stanford University, Stanford, California 94305, USA
    Genome Res 17:992-1004. 2007
    ..Many of these conserved repeats are also present in human, and are highly over-represented in predicted cis-regulatory modules. Seventy-six of the 83 families are present in chicken in addition to mammals...
  78. ncbi Evolutionary and biomedical insights from the rhesus macaque genome
    Richard A Gibbs
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    Science 316:222-34. 2007
    ..The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species...
  79. ncbi Mobile elements and mammalian genome evolution
    Prescott L Deininger
    Department of Environmental Health Sciences, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
    Curr Opin Genet Dev 13:651-8. 2003
    ....
  80. ncbi Mobile DNA elements in primate and human evolution
    Jinchuan Xing
    Department of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
    Am J Phys Anthropol . 2007
    ..Finally, these elements have had impacts on the genome itself. We review how they have influenced fundamental ongoing processes like nonhomologous recombination, genomic deletion, and X chromosome inactivation...
  81. ncbi Genome analysis of the platypus reveals unique signatures of evolution
    Wesley C Warren
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 453:175-83. 2008
    ..Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation...
  82. ncbi Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
    Tarjei S Mikkelsen
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 447:167-77. 2007
    ..A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation...
  83. ncbi 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
    ....
  84. ncbi Human genomic DNA quantitation system, H-Quant: development and validation for use in forensic casework
    Jaiprakash G Shewale
    ReliaGene Technologies, Inc, 5525 Mounes St Suite 101, New Orleans, LA 70123, USA
    J Forensic Sci 52:364-70. 2007
    ..Development and validation studies were performed on the 7500 real-time PCR system following the Quality Assurance Standards for Forensic DNA Testing Laboratories...
  85. ncbi Allelic heterogeneity in LINE-1 retrotransposition activity
    Sheila M Lutz
    Departments of Human Genetics and Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109 0618, USA
    Am J Hum Genet 73:1431-7. 2003
    ..2A retrotransposition efficiency. Thus, common L1 alleles can vary widely in their retrotransposition potential. We propose that such allelic heterogeneity can influence the potential L1 mutational load present in an individual genome...
  86. ncbi Identification of repeat structure in large genomes using repeat probability clouds
    Wanjun Gu
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
    Anal Biochem 380:77-83. 2008
    ..This method should be extremely useful as a tool for use in de novo identification of repeat structure in large newly sequenced genomes...