Batzer, Mark A. - Department of Biological Sciences, Louisiana State University

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Batzer, Mark A. - Department of Biological Sciences, Louisiana State University

Alu Recombination-Mediated Structural Deletions in the Chimpanzee Genome
Structure, diversity, and evolution of the 45-bp VNTR in intron 5 of the USH1C gene
Vol. 60, No. 2INFECTION AND IMMUNITY, Feb. 1992, p. 542-549 0019-9567/92/020542-08$02.00/0
Nucleic Acids Research, Vol. 19, No. 13 3619-3623 Amplification dynamics of human-specific (HS) alu family
Mammalian Retroelements Prescott L. Deininger1,2,4
Genetica 94: 1-8, 1994. 1 (g)1994KluwerAcademicPublishers. Printedin theNetherlands.
ELSEVIER Gene205(1997) 161-171 GENEAN INTERNATIONAL JOURNAL ON
Development of a serum profile for healthy aging Lauri O. Byerley & Larry Leamy & Sun W. Tam &
Residential College Must be entering freshman majoring in: biochemistry; biological sciences;
DOI: 10.1126/science.1139247 , 222 (2007);316Science
Genome analysis of the platypus reveals unique signatures of evolution
INT'L. J. AGING AND HUMAN DEVELOPMENT, Vol. 63(4) 317-334, 2006 KNOWLEDGE OF MEMORY AGING IN ADULTHOOD*
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Copyright 2001 by the Genetics Society of America Alu Insertion Polymorphisms for the Study of Human Genomic Diversity
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6 Lynch, M. and Conery, J.S. (2000) The evolutionary fate and consequences of duplicate genes. Science 290, 11511155
105:495-501, 2008. First published Jun 12, 2008; doi:10.1152/japplphysiol.90450.2008J Appl Physiol Louisiana Healthy Aging Study
ARTICLE doi:10.1038/nature09708 Mapping copy number variation by
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Copyright 2007 by the Genetics Society of America DOI: 10.1534/genetics.106.067355
Mutation Research, 207 (1988) 53-56 53 Molecular analysis of Drosophilamelanogaster.4dhnLA405 confirms reliability
Accessory Tables Table A1. C-values vs genome size.
Molecular phylogenetic analyses of genus Crocodylus (Eusuchia, Crocodylia, Crocodylidae) and the taxonomic position of Crocodylus porosus
Differential Alu Mobilization and Polymorphism Among the Human and Chimpanzee Lineages
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Chromosomal Inversions between Human and Chimpanzee Lineages Caused by Retrotransposons
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Metabolic syndrome and risk factors for cardiovascular disease: are nonagenarians protected?
Nucleic Acids Research, Vol. 19, No. 18 5081 Enhanced evolutionar PCR using oligonucleotides with
Fax +41 61 306 12 34 E-Mail karger@karger.ch
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Molecular Phylogenetics and Evolution 37 (2005) 872880 www.elsevier.com/locate/ympev
Abstract Recently, mutations in USH1C were shown to be associated with Usher syndrome type IC, and a muta-
Long interspersed elements (LINE-1s) are abundant retro-transposons in mammalian genomes that probably retro-
Evolution of Retroposons PRESCOTT L. DEININGER and MARK A. BATZER
Comprehensive Analysis of Two Alu Yd Subfamilies Jinchuan Xing,1
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Volff J-N (ed): Genome and Disease. Genome Dyn. Basel, Karger, 2006, vol 1, pp 104115
Genome of the marsupial Monodelphis domestica reveals innovation in
Diversity of Retrotransposable Elements Cytogenet Genome Res 110:537542 (2005)
Transposable elements (TEs; also known as `jumping genes') are discrete pieces of DNA that can move within
BOOK REVIEWS Comprehensive Organic Transformations: A Guide to Func-
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6 Journal of Geriatric Physical Therapy Vol.30;1:07 Age-related Deterioration in Flexibility is Associated
Curriculum Vitae Kyudong Han
Human DNA quantitation using Alu element-based polymerase chain reaction
Published online 21 May 2007 Nucleic Acids Research, 2007, Vol. 35, No. 11 37413751 doi:10.1093/nar/gkm317
Genome-wide analysis of the human Alu Yb-lineage
PHS 398/2590 (Rev. 11/07) Page 1 Biographical Sketch Format Page Program Director/Principal Investigator (Batzer, Mark A.)
THOMAS JOSHUA MEYER Department of Biological Sciences
George W. Cook, Jr. University of Arkansas, Fayetteville, Arkansas -BS Chemical Engineering, 1975
LINEs and SINEs of Primate Evolution MIRIAM K. KONKEL, JERILYN A. WALKER, AND MARK A. BATZER
Health Care for Women International, 31:9971012, 2010 Copyright Taylor & Francis Group, LLC
Computational Methods for the Analysis of Primate Mobile Richard Cordaux, Shurjo K. Sen, Miriam K. Konkel, and Mark A. Batzer
Laboratory Methods for the Analysis of Primate Mobile Elements
RESEARCH Open Access Heads or tails: L1 insertion-associated 5'
study of universal patterns of evolution such as the distri-bution of evolutionary rates of orthologous genes, which is
EPIDEMIOLOGY Distribution of Four HIV Type 1-Resistance Polymorphisms
Internal priming: An opportunistic pathway for L1 and Alu retrotransposition in hominins
Phylogeny of the macaques (Cercopithecidae: Macaca) based on Alu elements Jing Li a,b
10.1101/gr.091827.109Access the most recent version at doi: 2009 19: 1516-1526 originally published online May 13, 2009Genome Res.
BioMed Central Page 1 of 5
BioMed Central Page 1 of 4
An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair
GENE was founded in 1976 by Professor Waclaw Szybalski, who guided the journal as Editor-in-Chief for nearly 20 years. In 1996
L1 recombination-associated deletions generate human genomic variation
Identification of repeat structure in large genomes using repeat probability clouds Wanjun Gu a
Table of Contents 1. Supplementary Notes S1-S24
Figure A1. Describes format followed for read depth distribution. Figure A2. Read depth on contig base pairs.
Evolutionary Emergence of Genes Through
Biometrics DOI: 10.1111/j.1541-0420.2007.00801.x Exact Sample Size Needed to Detect Dependence in 2 2 2 Tables
Physical Activity Level and Physical Functionality in Nonagenarians Compared to Individuals
Aging, Resting Metabolic Rate, and Oxidative Damage: Results From the Louisiana Healthy Aging Study
Short Communication In search of polymorphic Alu insertions with restricted
SINEs, evolution and genome structure in the opossum Wanjun Gu a,1
DOI: 10.1126/science.1139462 , 238 (2007);316Science
Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons
Introduction for the Gene special issue dedicated to the meeting "Genomic impact of eukaryotic transposable elements" at Asilomar
Mutation Research 616 (2007) 175180 Distribution of the HIV resistance CCR5-32 allele
Emergence of primate genes by retrotransposon-mediated sequence transduction
www.ajhg.org The American Journal of Human Genetics Volume 79 July 2006 41 Human Genomic Deletions Mediated by Recombination
Annals of Human Biology, MarchApril 2006; 33(2): 142160 ORIGINAL ARTICLE
Estimating the retrotransposition rate of human Alu elements Richard Cordaux, Dale J. Hedges, Scott W. Herke, Mark A. Batzer
Recently integrated Alu retrotransposons are essentially neutral residents of the human genome
HUMAN MUTATION 27(4), 323^329, 2006 dbRIP: A Highly Integrated Database
BioMed Central Page 1 of 7
CD8 T-cell immune phenotype of successful aging Hui-Chen Hsu a
SVA Elements: A Hominid-specific Retroposon Family Hui Wang, Jinchuan Xing, Deepak Grover, Dale J. Hedges
Original Article Physical Function and Quality of Life in Older
Modeling the Amplification Dynamics of Human Alu Retrotransposons
Under the genomic radar: The Stealth model of Alu amplification
Notes & Tips Resolution of mixed human DNA samples using mitochondrial
Am. J. Hum. Genet. 73:9941015, 2003 Haplotypes in the Dystrophin DNA Segment Point to a Mosaic Origin
Alignment Workspace of Old and new Yb8 CpG Comp Y.meg ClustalV (Weighted) Page 1 Wednesday, August 07, 2002 5:32 PM
Alignment Workspace of YC1 CpG Y.meg ClustalV (Weighted) Page 1 Wednesday, August 07, 2002 5:36 PM
Alignment Workspace of Untitled ClustalV (Weighted) Page 1 Wednesday, August 07, 2002 5:43 PM
Following the LINEs: An Analysis of Primate Genomic Variation at Human-Specific LINE-1 Insertion Sites
Quantitative intra-short interspersed element PCR for species-specific DNA identification
Y Chromosome STR Haplotypes and the Genetic Structure of U.S. Populations
Alu insertions versus blood group plus protein genetic variability in four Amerindian populations1
370 | MAY 2002 | VOLUME 3 www.nature.com/reviews/genetics R E V I E W S
Non-traditional Alu evolution and Primate Genomic Diversity
Mutation Research Genomics 458 (2001) 5570 Comprehensive analysis of a large genomic sequence at the
Evidence for alternate splicing within the mRNA transcript encoding the DNA damage response kinase ATR
BOOK REVIEWS Methods in Molecular Biology, Volume 151, Matrix Metallo-
Alu insertion polymorphisms and the genetic structure of human populations from the Caucasus
Phylogenetic Analysis of the Friedreich Ataxia GAA Trinucleotide Repeat Cristina M. Justice,1,
Potential Gene Conversion and Source Genes for Recently Integrated Alu Elements
Reading between the LINEs: Human Genomic Variation Induced by LINE-1 Retrotransposition
Am. J. Hum. Genet. 66:979988, 2000 The Distribution of Human Genetic Diversity: A Comparison
Genetica 107: 149161, 1999. 2000 Kluwer Academic Publishers. Printed in the Netherlands.
Am. J. Hum. Genet. 63:18391851, 1998 Estimating African American Admixture Proportions by Use of Population-
Am. J. Hum. Genet. 63:18071823, 1998 Genetic Evidence for the Proto-Austronesian Homeland in Asia: mtDNA
Rapid report Assembly of a high-resolution map of the Acadian Usher syndrome
Proc. Natl. Acad. Sci. USA Vol. 95, pp. 19611967, February 1998
Genetic Structure of the Ancestral Population of Modern Humans Ewa Zietkiewicz,1
Alu Insertion Polymorphisms and Human Evolution: Evidence for a Larger Population
Point Counter Point Further Comments on
Abstract The EWS gene has been identified as being systematically translocated in Ewing's sarcoma. In order
I Mol Evol(1996)42:1 jou..oMOLECULAR
Standardized Nomenclature for Alu Repeats Mark A. Batzer,1
Hum Genet (1995) 95:363-364 9 Springer-Verlag 1995 David H. Kass -Mark A. Batzer 9Prescott L. Deininger
J. Mol. Biol. (1995) 247, 418427 Dispersion and Insertion Polymorphism in Two Small
1596 G . E. Novick et a/. Electrophoresis 1995, 16, 1596-1601 Gabriel E. Novick'
GATA 11(2): 34--38, 1994 A Consensus Alu Repeat Probe
1993 Oxford University Press Human Molecular Genetics, Vol. 2, No. 3 299-304 Structure and genomic sequence of the myotonic
Mutation Research, 199 (1988) 255-268 Spectra of molecular changes induced in DNA of Drosophila spermatozoa
Birth of a chimeric primate gene by capture of the transposase gene from a mobile element
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Plate Protocol: Precipitation of 10-l Sequencing Reactions (01-14-11) 1) Remove 96-well plate [Note #1] from thermocycler; spin (3800 rpm or 2500 RCF; 1 min).
Tube Protocol: Precipitation of 10-l Sequencing Reactions (01-14-11) This protocol is based on an ABI 96-well plate protocol. Better results are easier to obtain with plates and a
Why LSU Science? ChoiCe of 8 Majors Biochemistry
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Success Story of Louisiana
Am. J. Hum. Genet. 72:578589, 2003 Human Population Genetic Structure and Inference of Group Membership
Sequential Loss of Two Neighboring Exons of the Tropoelastin Gene During Primate Evolution
cDNAs Derived from Primary and Small Cytoplasmic Alu (scAlu) Transcripts
From the margins of the genome: mobile elements shape
Rapid report The mouse deafness locus (dn) is associated with an inversion on
doi: 10.1046/j.1529-8817.2005.00163.x Worldwide Genetic Variation at the 3 -UTR Region of
Evolution of Human Retrosequences: Alu
7956 Structure of ideas in classic writings 8018 Generating knockout mice with gonadal stem cells
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Mikkelsen et al. "Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences"
Mutation Research 501 (2002) 137141 Short communication
Comparative Genomics and Molecular Evolution Cytogenet Genome Res 108:6372 (2005)
Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies
Genome Databases Marion L Carroll,Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
Perspective Reading TE leaves: New approaches to the
RESEARCH ARTICLE Dietary differences between centenarians residing
Genetic Variation of Recent Alu Insertions in Human Populations Mark A. Batzer,1
Large-scale Analysis of the Alu Ya5 and Yb8 Subfamilies and their Contribution to Human
Mobile DNA Elements in Primate and Human Evolution Jinchuan Xing,1
BioMed Central Page 1 of 10
Mutation Research 616 (2007) 2433 Mobile element-based forensic genomics
Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms
BioMed Central Page 1 of 9
Straightening out the LINEs: LINE-1 orthologous loci$ Huei Jin Hoa
Analysis of the Human Alu Ya-lineage Anthony C. Otieno, Anthony B. Carter, Dale J. Hedges
Seminars in Cancer Biology 20 (2010) 211221 Contents lists available at ScienceDirect
LETTER doi:10.1038/nature09687 Comparative and demographic analysis of
Genome Sequence Analysis Margaret M DeAngelis, Louisiana State University Health Sciences Center,
Teaching an old dog new tricks: SINEs of canine genomic diversity
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A Guide to Preparing for Promotion and Tenure
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Active Alu Element "A-Tails": Size Does Matter Astrid M. Roy-Engel,1
www.sciencemag.org/cgi/content/full/316/5822/222/DC1 Supporting Online Material for
Ancestral Alleles and Population Origins: Inferences Depend on Mutation Rate Alan R. Rogers,* Stephen Wooding, Chad D. Huff,* Mark A. Batzer, and Lynn B. Jorde
Molecular Phylogenetics and Evolution 35 (2005) 117126 www.elsevier.com/locate/ympev
Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity
Nucleic Acids Research, Vol. 18, No. 23 6793 Structure and variability of recently inserted Alu family
Alu Repeats and Human Disease Prescott L. Deininger*,
ANALYTICAL BIOCHEMISTRY 244, 414 (1997) BOOK REVIEWS
Mutation Research 616 (2007) 12 This special issue is a tribute to Dr. Anthony "Tony"
Genetic Evidence on the Origins of Indian Caste Populations
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Cloning and Characterization of the Prostate-Specific Membrane Antigen Promoter
LINE-1 preTa Elements in the Human Genome Abdel-Halim Salem1,2
Notes & Tips Mobile element-based assay for human gender determination
Quantitative PCR for DNA identification based on genome-specific interspersed repetitive elements
Copyright 0 1997 by the Genetics Society of America Alu Evolution in Human Populations:Using the Coalescent to Estimate
Am. J. Hum. Genet. 73:14311437, 2003 Allelic Heterogeneity in LINE-1 Retrotransposition Activity
Am. J. Hum. Genet. 68:738752, 2001 Patterns of Ancestral Human Diversity: An Analysis of Alu-Insertion and
0.3 uM 0.5 uM 0.7 uM 1.0 uM 2.0 uM 5.0 uM A653 Ctr. Bench (top level) 24,000 1,520 445 260 115 25
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59-Transducing SVA retrotransposon groups spread efficiently throughout the human genome
CV_latest, Page 1 of 3 SHURJO KUMAR SEN
www.sciencemag.org/cgi/content/full/316/5822/238/DC1 Supporting Online Material for
Patterns of Human Diversity, within and among Continents, Inferred from Biallelic
L1HS2 alignment Alignment Report of 'Untitled' -ClustalW (Slow/Accurate, IUB) : Saturday, February 08, 2003 3:47 PM
Abstract An analysis of 11 Alu insertion polymorphisms (ACE, TPA25, PV92, APO, FXIIIB, D1, A25, B65, HS2.43,
Louisiana Biomedical Research Network -LBRN 2010 Competition for INBRE Research Project
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Modeling Human Evolution--To Tree or Not Stephen T. Sherry and Mark A. Batzer1
A Guide to Preparing for Promotion and Tenure
Alu elements and hominid phylogenetics Abdel-Halim Salem*
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Research from the Batzer Lab featured on the cover of Nature The genome sequence of the platypus (Ornithorhynchus anatinus) is unraveled in the May 8,
BioMed Central Page 1 of 11
Low levels of nucleotide diversity in Crocodylus moreletii and evidence of hybridization with C. acutus
The genome of a songbird Wesley C. Warren1
Chompy: An infestation of MITE-like repetitive elements in the crocodilian genome
Alignment Workspace of Untitled ClustalV (Weighted) Page 1 Wednesday, August 07, 2002 5:42 PM
Identification of three genomic haplotypes 50
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Comprehensive analysis of Alu-associated diversity on the human sex chromosomes
RESEARCH ARTICLE Personality and longevity: findings from the Georgia
TECHNICAL NOTE Jaiprakash G. Shewale,1
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RESEARCH ARTICLE Open Access Nuclear versus mitochondrial DNA: evidence for
Table of Contents SupplementalSectionS1GenomeSequencingandAssembly........................................... 2
Gene 215 (1998) 461469 Identification and mutation analysis of a cochlear-expressed, zinc finger
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Detection of t(11;14) Using Interphase Molecular Cytogenetics in Mantle Cell Lymphoma
Cancer Chemother Pharmacol (1986) 17:209-217 Original articles
[16] REPEATEDDNA SEQUENCES 213 [16] Evolutionary Analyses of Repetitive DNA
Genomic rearrangements by LINE-1 insertion-mediated deletion in the human
BIOCHEMISTRY Analytical Biochemistry 337 (2005) 8997
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Recently Integrated Alu Elements and Human Genomic Diversity Abdel-Halim Salem,* Gail E. Kilroy,* W. Scott Watkins, Lynn B. Jorde, and Mark A. Batzer*
Repair-Mediated Duplication by Capture of Proximal Chromosomal DNA Has Shaped Vertebrate Genome
High-resolution Cartography of Recently Integrated Human Chromosome 19-Specific Alu Fossils
Genetic Variation Among World Populations: Inferences From 100 Alu Insertion Polymorphisms
Mobile elements and mammalian genome evolution Prescott L Deininger
A SINE-based dichotomous key for primate identification Scott W. Herke a
Alu Retrotransposition-mediated Deletion Pauline A. Callinan1
Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica
Copyright 1999 by the Genetics Society of America Spatial and Temporal Distribution of the Neutral Polymorphisms in the Last
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43. E.-Y. Bergsdorf, A. A. Zdebik, T. J. Jentsch, J. Biol. Chem. 284, 11184 (2009).
A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans
Ceramide glycosylation catalyzed by glucosylceramide synthase is a critical process maintaining the stemness of
Supplemental Information Table of Contents
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Demographic history and rare allele sharing among human populations
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Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia
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Repetitive Elements May Comprise Over Two-Thirds of the Human Genome
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