Mark A Batzer

Mark A Batzer

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Mark A Batzer

Mark A Batzer

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Analysis of lineage-specific subfamilies in the genome of the olive baboon, .

Mob DNA 2018 19;9:10. Epub 2018 Mar 19.

Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803 USA.

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http://dx.doi.org/10.1186/s13100-018-0115-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5858127PMC
March 2018

Recently integrated insertions in the squirrel monkey () lineage and application for population analyses.

Mob DNA 2018 12;9. Epub 2018 Feb 12.

Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803 USA.

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http://dx.doi.org/10.1186/s13100-018-0114-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5808450PMC
February 2018

DNA methylation variation of human-specific Alu repeats.

Epigenetics 2016 18;11(2):163-73. Epub 2016 Feb 18.

a Department of Biological Sciences , Louisiana State University , Baton Rouge , LA , USA.

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http://dx.doi.org/10.1080/15592294.2015.1130518DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4846114PMC
December 2016

Discovery of a new repeat family in the Callithrix jacchus genome.

Genome Res 2016 05 25;26(5):649-59. Epub 2016 Feb 25.

Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA;

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http://dx.doi.org/10.1101/gr.199075.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864456PMC
May 2016

An integrated map of structural variation in 2,504 human genomes.

Nature 2015 Oct;526(7571):75-81

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature15394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617611PMC
October 2015

A comparison of 100 human genes using an alu element-based instability model.

PLoS One 2013 3;8(6):e65188. Epub 2013 Jun 3.

Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065188PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670932PMC
January 2015

Gibbon genome and the fast karyotype evolution of small apes.

Nature 2014 Sep;513(7517):195-201

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature13679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4249732PMC
September 2014

Tangram: a comprehensive toolbox for mobile element insertion detection.

BMC Genomics 2014 Sep 16;15:795. Epub 2014 Sep 16.

Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, USA.

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http://dx.doi.org/10.1186/1471-2164-15-795DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4180832PMC
September 2014

Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations.

Genome Res 2013 Jul 18;23(7):1170-81. Epub 2013 Apr 18.

Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA.

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http://dx.doi.org/10.1101/gr.148973.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3698510PMC
July 2013

An alu-based phylogeny of lemurs (infraorder: Lemuriformes).

PLoS One 2012 28;7(8):e44035. Epub 2012 Aug 28.

Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044035PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3429421PMC
February 2013

Genomic impact of eukaryotic transposable elements.

Mob DNA 2012 Nov 21;3(1):19. Epub 2012 Nov 21.

Institute of Experimental Pathology, ZMBE, University of Münster, Münster D-48149, Germany.

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http://dx.doi.org/10.1186/1759-8753-3-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3520738PMC
November 2012

Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers.

Mob DNA 2012 Apr 30;3. Epub 2012 Apr 30.

Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1186/1759-8753-3-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357318PMC
April 2012

Repetitive elements may comprise over two-thirds of the human genome.

PLoS Genet 2011 Dec 1;7(12):e1002384. Epub 2011 Dec 1.

Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, Colorado, USA.

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http://dx.doi.org/10.1371/journal.pgen.1002384DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228813PMC
December 2011

Alu pair exclusions in the human genome.

Mob DNA 2011 Sep 23;2:10. Epub 2011 Sep 23.

Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA.

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http://dx.doi.org/10.1186/1759-8753-2-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3215922PMC
September 2011

Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia.

Gene 2011 Jun 17;478(1-2):35-41. Epub 2011 Feb 17.

National DNA Analysis Centre, Central Forensic Science Laboratory, 30, Gorachand Road, Park Circus, Kolkata 700 014, West Bengal, India.

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http://dx.doi.org/10.1016/j.gene.2011.01.012DOI Listing
June 2011

Reading TE leaves: new approaches to the identification of transposable element insertions.

Genome Res 2011 Jun;21(6):813-20

Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi State, Mississippi 39762, USA.

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https://biosci-batzerlab.biology.lsu.edu/Publications/Ray_an
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http://genome.cshlp.org/cgi/doi/10.1101/gr.110528.110
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http://dx.doi.org/10.1101/gr.110528.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106314PMC
June 2011

Comparative and demographic analysis of orang-utan genomes.

Authors:
Devin P Locke LaDeana W Hillier Wesley C Warren Kim C Worley Lynne V Nazareth Donna M Muzny Shiaw-Pyng Yang Zhengyuan Wang Asif T Chinwalla Pat Minx Makedonka Mitreva Lisa Cook Kim D Delehaunty Catrina Fronick Heather Schmidt Lucinda A Fulton Robert S Fulton Joanne O Nelson Vincent Magrini Craig Pohl Tina A Graves Chris Markovic Andy Cree Huyen H Dinh Jennifer Hume Christie L Kovar Gerald R Fowler Gerton Lunter Stephen Meader Andreas Heger Chris P Ponting Tomas Marques-Bonet Can Alkan Lin Chen Ze Cheng Jeffrey M Kidd Evan E Eichler Simon White Stephen Searle Albert J Vilella Yuan Chen Paul Flicek Jian Ma Brian Raney Bernard Suh Richard Burhans Javier Herrero David Haussler Rui Faria Olga Fernando Fleur Darré Domènec Farré Elodie Gazave Meritxell Oliva Arcadi Navarro Roberta Roberto Oronzo Capozzi Nicoletta Archidiacono Giuliano Della Valle Stefania Purgato Mariano Rocchi Miriam K Konkel Jerilyn A Walker Brygg Ullmer Mark A Batzer Arian F A Smit Robert Hubley Claudio Casola Daniel R Schrider Matthew W Hahn Victor Quesada Xose S Puente Gonzalo R Ordoñez Carlos López-Otín Tomas Vinar Brona Brejova Aakrosh Ratan Robert S Harris Webb Miller Carolin Kosiol Heather A Lawson Vikas Taliwal André L Martins Adam Siepel Arindam Roychoudhury Xin Ma Jeremiah Degenhardt Carlos D Bustamante Ryan N Gutenkunst Thomas Mailund Julien Y Dutheil Asger Hobolth Mikkel H Schierup Oliver A Ryder Yuko Yoshinaga Pieter J de Jong George M Weinstock Jeffrey Rogers Elaine R Mardis Richard A Gibbs Richard K Wilson

Nature 2011 Jan;469(7331):529-33

The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature09687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060778PMC
January 2011

LINEs and SINEs of primate evolution.

Evol Anthropol 2010 Nov;19(6):236-249

Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1002/evan.20283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137791PMC
November 2010

Molecular phylogenetic analyses of genus Crocodylus (Eusuchia, Crocodylia, Crocodylidae) and the taxonomic position of Crocodylus porosus.

Mol Phylogenet Evol 2010 Oct 19;57(1):393-402. Epub 2010 Jun 19.

National DNA Analysis Centre, Central Forensic Science Laboratory, Park Circus, Kolkata, West Bengal, India.

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http://dx.doi.org/10.1016/j.ympev.2010.06.011DOI Listing
October 2010

A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome.

Semin Cancer Biol 2010 Aug 20;20(4):211-21. Epub 2010 Mar 20.

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1016/j.semcancer.2010.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2925057PMC
August 2010

Mobile element scanning (ME-Scan) by targeted high-throughput sequencing.

BMC Genomics 2010 Jun 30;11:410. Epub 2010 Jun 30.

Dept. of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA.

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http://dx.doi.org/10.1186/1471-2164-11-410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996938PMC
June 2010

Computational methods for the analysis of primate mobile elements.

Methods Mol Biol 2010 ;628:137-51

Laboratoire Ecologie, Evolution et Symbiose, CNRS UMR 6556, Universitè de Poitiers, Poitiers, France.

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http://dx.doi.org/10.1007/978-1-60327-367-1_8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880165PMC
May 2010

Laboratory methods for the analysis of primate mobile elements.

Methods Mol Biol 2010 ;628:153-79

Department of Biology, West Virginia University, Morgantown, WV, USA.

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http://dx.doi.org/10.1007/978-1-60327-367-1_9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880178PMC
May 2010

The genome of a songbird.

Nature 2010 Apr;464(7289):757-62

The Genome Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature08819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187626PMC
April 2010

Heads or tails: L1 insertion-associated 5' homopolymeric sequences.

Mob DNA 2010 Feb 1;1(1). Epub 2010 Feb 1.

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Bldg, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1186/1759-8753-1-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2837659PMC
February 2010

Phylogeny of the macaques (Cercopithecidae: Macaca) based on Alu elements.

Gene 2009 Dec 2;448(2):242-9. Epub 2009 Jun 2.

Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana 70803, USA.

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http://dx.doi.org/10.1016/j.gene.2009.05.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783879PMC
December 2009

Internal priming: an opportunistic pathway for L1 and Alu retrotransposition in hominins.

Gene 2009 Dec 6;448(2):233-41. Epub 2009 Jun 6.

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1016/j.gene.2009.05.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784234PMC
December 2009

5'-Transducing SVA retrotransposon groups spread efficiently throughout the human genome.

Genome Res 2009 Nov 3;19(11):1992-2008. Epub 2009 Aug 3.

Fachgebiet PR2/Retroelemente, Paul-Ehrlich-Institut, D-63225 Langen, Germany.

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http://dx.doi.org/10.1101/gr.093435.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775593PMC
November 2009

Reading between the LINEs to see into the past.

Trends Genet 2009 Nov;25(11):475-9

Department of Biochemistry and Molecular Biology, Box 9650, Mississippi State University, Mississippi State, MS 39762, USA.

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http://dx.doi.org/10.1016/j.tig.2009.09.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783679PMC
November 2009

Alu repeats increase local recombination rates.

BMC Genomics 2009 Nov 16;10:530. Epub 2009 Nov 16.

Dept. of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA.

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http://dx.doi.org/10.1186/1471-2164-10-530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2785838PMC
November 2009

The impact of retrotransposons on human genome evolution.

Nat Rev Genet 2009 Oct;10(10):691-703

CNRS UMR 6556 Ecologie, Evolution, Symbiose, Université de Poitiers, 40 Avenue du Recteur Pineau, Poitiers, France.

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http://www.nature.com/articles/nrg2640
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http://dx.doi.org/10.1038/nrg2640DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2884099PMC
October 2009

Distribution of four HIV type 1-resistance polymorphisms (CCR5-Delta32, CCR5-m303, CCR2-64I, and SDF1-3'A) in the Bahraini population.

AIDS Res Hum Retroviruses 2009 Oct;25(10):973-7

Department of Anatomy, College of Medicine and Medical Sciences, Arabian Gulf University, Kingdom of Bahrain.

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http://dx.doi.org/10.1089/aid.2009.0066DOI Listing
October 2009

Mobile elements create structural variation: analysis of a complete human genome.

Genome Res 2009 Sep 13;19(9):1516-26. Epub 2009 May 13.

Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84109, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.091827.109
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http://dx.doi.org/10.1101/gr.091827.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752133PMC
September 2009

High frequency of the D allele of the angiotensin-converting enzyme gene in Arabic populations.

BMC Res Notes 2009 Jun 8;2:99. Epub 2009 Jun 8.

Department of Anatomy, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Kingdom of Bahrain.

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http://dx.doi.org/10.1186/1756-0500-2-99DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2699340PMC
June 2009

Repair-mediated duplication by capture of proximal chromosomal DNA has shaped vertebrate genome evolution.

PLoS Genet 2009 May 8;5(5):e1000469. Epub 2009 May 8.

Department of Biology, University of Texas at Arlington, Arlington, TX, USA.

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http://dx.doi.org/10.1371/journal.pgen.1000469DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2671141PMC
May 2009

Allele frequencies of the human platelet antigen-1 in the Egyptian population.

BMC Res Notes 2009 May 20;2:90. Epub 2009 May 20.

Department of Anatomy, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Kingdom of Bahrain.

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http://dx.doi.org/10.1186/1756-0500-2-90DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2691742PMC
May 2009

An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair.

Genomics 2009 Mar 11;93(3):205-12. Epub 2008 Nov 11.

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1016/j.ygeno.2008.09.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2672417PMC
March 2009

Chromosomal inversions between human and chimpanzee lineages caused by retrotransposons.

PLoS One 2008 29;3(12):e4047. Epub 2008 Dec 29.

Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0004047PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2603318PMC
March 2009

L1 recombination-associated deletions generate human genomic variation.

Proc Natl Acad Sci U S A 2008 Dec 26;105(49):19366-71. Epub 2008 Nov 26.

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0807866105
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http://dx.doi.org/10.1073/pnas.0807866105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614767PMC
December 2008

Identification of repeat structure in large genomes using repeat probability clouds.

Anal Biochem 2008 Sep 20;380(1):77-83. Epub 2008 May 20.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1016/j.ab.2008.05.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2533575PMC
September 2008

Genome analysis of the platypus reveals unique signatures of evolution.

Authors:
Wesley C Warren LaDeana W Hillier Jennifer A Marshall Graves Ewan Birney Chris P Ponting Frank Grützner Katherine Belov Webb Miller Laura Clarke Asif T Chinwalla Shiaw-Pyng Yang Andreas Heger Devin P Locke Pat Miethke Paul D Waters Frédéric Veyrunes Lucinda Fulton Bob Fulton Tina Graves John Wallis Xose S Puente Carlos López-Otín Gonzalo R Ordóñez Evan E Eichler Lin Chen Ze Cheng Janine E Deakin Amber Alsop Katherine Thompson Patrick Kirby Anthony T Papenfuss Matthew J Wakefield Tsviya Olender Doron Lancet Gavin A Huttley Arian F A Smit Andrew Pask Peter Temple-Smith Mark A Batzer Jerilyn A Walker Miriam K Konkel Robert S Harris Camilla M Whittington Emily S W Wong Neil J Gemmell Emmanuel Buschiazzo Iris M Vargas Jentzsch Angelika Merkel Juergen Schmitz Anja Zemann Gennady Churakov Jan Ole Kriegs Juergen Brosius Elizabeth P Murchison Ravi Sachidanandam Carly Smith Gregory J Hannon Enkhjargal Tsend-Ayush Daniel McMillan Rosalind Attenborough Willem Rens Malcolm Ferguson-Smith Christophe M Lefèvre Julie A Sharp Kevin R Nicholas David A Ray Michael Kube Richard Reinhardt Thomas H Pringle James Taylor Russell C Jones Brett Nixon Jean-Louis Dacheux Hitoshi Niwa Yoko Sekita Xiaoqiu Huang Alexander Stark Pouya Kheradpour Manolis Kellis Paul Flicek Yuan Chen Caleb Webber Ross Hardison Joanne Nelson Kym Hallsworth-Pepin Kim Delehaunty Chris Markovic Pat Minx Yucheng Feng Colin Kremitzki Makedonka Mitreva Jarret Glasscock Todd Wylie Patricia Wohldmann Prathapan Thiru Michael N Nhan Craig S Pohl Scott M Smith Shunfeng Hou Mikhail Nefedov Pieter J de Jong Marilyn B Renfree Elaine R Mardis Richard K Wilson

Nature 2008 May;453(7192):175-83

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature06936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803040PMC
May 2008

Mobile DNA elements in primate and human evolution.

Am J Phys Anthropol 2007 ;Suppl 45:2-19

Department of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA.

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http://dx.doi.org/10.1002/ajpa.20722DOI Listing
January 2008

Alu recombination-mediated structural deletions in the chimpanzee genome.

PLoS Genet 2007 Oct 10;3(10):1939-49. Epub 2007 Sep 10.

Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA.

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http://dx.plos.org/10.1371/journal.pgen.0030184
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http://dx.doi.org/10.1371/journal.pgen.0030184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2041999PMC
October 2007

SINEs, evolution and genome structure in the opossum.

Gene 2007 Jul 19;396(1):46-58. Epub 2007 Mar 19.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1016/j.gene.2007.02.028DOI Listing
July 2007

Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica.

Genome Res 2007 Jul 10;17(7):992-1004. Epub 2007 May 10.

Department of Radiology, School of Medicine, Stanford University, Stanford, California 94305, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.6070707
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http://dx.doi.org/10.1101/gr.6070707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899126PMC
July 2007

In search of polymorphic Alu insertions with restricted geographic distributions.

Genomics 2007 Jul 11;90(1):154-8. Epub 2007 May 11.

Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1016/j.ygeno.2007.03.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2045505PMC
July 2007

Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome.

Nucleic Acids Res 2007 21;35(11):3741-51. Epub 2007 May 21.

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkm317DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920257PMC
July 2007

Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies.

Gene 2007 Apr 30;390(1-2):28-38. Epub 2006 Aug 30.

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.

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http://dx.doi.org/10.1016/j.gene.2006.07.040DOI Listing
April 2007

Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons.

Gene 2007 Apr 16;390(1-2):18-27. Epub 2006 Sep 16.

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.

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http://dx.doi.org/10.1016/j.gene.2006.08.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1847406PMC
April 2007

A SINE-based dichotomous key for primate identification.

Gene 2007 Apr 30;390(1-2):39-51. Epub 2006 Aug 30.

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.

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http://dx.doi.org/10.1016/j.gene.2006.08.015DOI Listing
April 2007

Evolutionary and biomedical insights from the rhesus macaque genome.

Authors:
Richard A Gibbs Jeffrey Rogers Michael G Katze Roger Bumgarner George M Weinstock Elaine R Mardis Karin A Remington Robert L Strausberg J Craig Venter Richard K Wilson Mark A Batzer Carlos D Bustamante Evan E Eichler Matthew W Hahn Ross C Hardison Kateryna D Makova Webb Miller Aleksandar Milosavljevic Robert E Palermo Adam Siepel James M Sikela Tony Attaway Stephanie Bell Kelly E Bernard Christian J Buhay Mimi N Chandrabose Marvin Dao Clay Davis Kimberly D Delehaunty Yan Ding Huyen H Dinh Shannon Dugan-Rocha Lucinda A Fulton Ramatu Ayiesha Gabisi Toni T Garner Jennifer Godfrey Alicia C Hawes Judith Hernandez Sandra Hines Michael Holder Jennifer Hume Shalini N Jhangiani Vandita Joshi Ziad Mohid Khan Ewen F Kirkness Andrew Cree R Gerald Fowler Sandra Lee Lora R Lewis Zhangwan Li Yih-Shin Liu Stephanie M Moore Donna Muzny Lynne V Nazareth Dinh Ngoc Ngo Geoffrey O Okwuonu Grace Pai David Parker Heidie A Paul Cynthia Pfannkoch Craig S Pohl Yu-Hui Rogers San Juana Ruiz Aniko Sabo Jireh Santibanez Brian W Schneider Scott M Smith Erica Sodergren Amanda F Svatek Teresa R Utterback Selina Vattathil Wesley Warren Courtney Sherell White Asif T Chinwalla Yucheng Feng Aaron L Halpern Ladeana W Hillier Xiaoqiu Huang Pat Minx Joanne O Nelson Kymberlie H Pepin Xiang Qin Granger G Sutton Eli Venter Brian P Walenz John W Wallis Kim C Worley Shiaw-Pyng Yang Steven M Jones Marco A Marra Mariano Rocchi Jacqueline E Schein Robert Baertsch Laura Clarke Miklós Csürös Jarret Glasscock R Alan Harris Paul Havlak Andrew R Jackson Huaiyang Jiang Yue Liu David N Messina Yufeng Shen Henry Xing-Zhi Song Todd Wylie Lan Zhang Ewan Birney Kyudong Han Miriam K Konkel Jungnam Lee Arian F A Smit Brygg Ullmer Hui Wang Jinchuan Xing Richard Burhans Ze Cheng John E Karro Jian Ma Brian Raney Xinwei She Michael J Cox Jeffery P Demuth Laura J Dumas Sang-Gook Han Janet Hopkins Anis Karimpour-Fard Young H Kim Jonathan R Pollack Tomas Vinar Charles Addo-Quaye Jeremiah Degenhardt Alexandra Denby Melissa J Hubisz Amit Indap Carolin Kosiol Bruce T Lahn Heather A Lawson Alison Marklein Rasmus Nielsen Eric J Vallender Andrew G Clark Betsy Ferguson Ryan D Hernandez Kashif Hirani Hildegard Kehrer-Sawatzki Jessica Kolb Shobha Patil Ling-Ling Pu Yanru Ren David Glenn Smith David A Wheeler Ian Schenck Edward V Ball Rui Chen David N Cooper Belinda Giardine Fan Hsu W James Kent Arthur Lesk David L Nelson William E O'brien Kay Prüfer Peter D Stenson James C Wallace Hui Ke Xiao-Ming Liu Peng Wang Andy Peng Xiang Fan Yang Galt P Barber David Haussler Donna Karolchik Andy D Kern Robert M Kuhn Kayla E Smith Ann S Zwieg

Science 2007 Apr;316(5822):222-34

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1126/science.1139247DOI Listing
April 2007

Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome.

Science 2007 Apr;316(5822):238-40

Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Multi-Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1126/science.1139462DOI Listing
April 2007

Mobile element-based forensic genomics.

Mutat Res 2007 Mar 8;616(1-2):24-33. Epub 2006 Dec 8.

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1016/j.mrfmmm.2006.11.019DOI Listing
March 2007

Distribution of the HIV resistance CCR5-Delta32 allele among Egyptians and Syrians.

Mutat Res 2007 Mar 12;616(1-2):175-80. Epub 2006 Dec 12.

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.

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http://dx.doi.org/10.1016/j.mrfmmm.2006.11.024DOI Listing
March 2007

Human genomic DNA quantitation system, H-Quant: development and validation for use in forensic casework.

J Forensic Sci 2007 Mar;52(2):364-70

ReliaGene Technologies, Inc., 5525 Mounes St. Suite 101, New Orleans, LA 70123, USA.

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http://dx.doi.org/10.1111/j.1556-4029.2006.00369.xDOI Listing
March 2007

A mobile element-based evolutionary history of guenons (tribe Cercopithecini).

BMC Biol 2007 Jan 31;5. Epub 2007 Jan 31.

Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Multi-scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1186/1741-7007-5-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797000PMC
January 2007

SINEs of a nearly perfect character.

Syst Biol 2006 Dec;55(6):928-35

Department of Biology, West Virginia University, PO Box 6057, Morgantown, West Virginia 26506, USA.

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http://dx.doi.org/10.1080/10635150600865419DOI Listing
December 2006

Emergence of primate genes by retrotransposon-mediated sequence transduction.

Proc Natl Acad Sci U S A 2006 Nov 13;103(47):17608-13. Epub 2006 Nov 13.

Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1073/pnas.0603224103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1693794PMC
November 2006

Alu insertion polymorphisms in Native Americans and related Asian populations.

Ann Hum Biol 2006 Mar-Apr;33(2):142-60

Centro de Biologia Genômica e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Faculdade de Biociências, Porto Alegre, RS, Brazil.

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http://dx.doi.org/10.1080/03014460500487347DOI Listing
October 2006

Human genomic deletions mediated by recombination between Alu elements.

Am J Hum Genet 2006 Jul 3;79(1):41-53. Epub 2006 May 3.

Department of Biological Sciences, Louisiana State University, Baton Rouge, 70803, USA.

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http://dx.doi.org/10.1086/504600DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1474114PMC
July 2006

Estimating the retrotransposition rate of human Alu elements.

Gene 2006 May 7;373:134-7. Epub 2006 Mar 7.

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1016/j.gene.2006.01.019DOI Listing
May 2006

Recently integrated Alu retrotransposons are essentially neutral residents of the human genome.

Gene 2006 May 9;373:138-44. Epub 2006 Mar 9.

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1016/j.gene.2006.01.020DOI Listing
May 2006

Birth of a chimeric primate gene by capture of the transposase gene from a mobile element.

Proc Natl Acad Sci U S A 2006 May 3;103(21):8101-6. Epub 2006 May 3.

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.

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http://dx.doi.org/10.1073/pnas.0601161103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1472436PMC
May 2006

dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans.

Hum Mutat 2006 Apr;27(4):323-9

Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York 14263, USA.

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http://dx.doi.org/10.1002/humu.20307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855216PMC
April 2006

Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity.

Proc Natl Acad Sci U S A 2006 Apr 17;103(17):6611-6. Epub 2006 Apr 17.

Department of Genetics, Division of Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1073/pnas.0601324103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1458931PMC
April 2006

Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms.

Gene 2006 Jan 10;365:11-20. Epub 2006 Jan 10.

Department of Cancer Genetics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA.

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http://dx.doi.org/10.1016/j.gene.2005.09.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1847407PMC
January 2006

Teaching an old dog new tricks: SINEs of canine genomic diversity.

Proc Natl Acad Sci U S A 2006 Jan 23;103(5):1157-8. Epub 2006 Jan 23.

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.

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http://dx.doi.org/10.1073/pnas.0510714103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1360598PMC
January 2006

A mobile element based phylogeny of Old World monkeys.

Mol Phylogenet Evol 2005 Dec 3;37(3):872-80. Epub 2005 Jun 3.

Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Multi-scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1016/j.ympev.2005.04.015DOI Listing
December 2005

Chompy: an infestation of MITE-like repetitive elements in the crocodilian genome.

Gene 2005 Dec 23;362:1-10. Epub 2005 Sep 23.

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.

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http://dx.doi.org/10.1016/j.gene.2005.07.010DOI Listing
December 2005

SVA elements: a hominid-specific retroposon family.

J Mol Biol 2005 Dec 19;354(4):994-1007. Epub 2005 Oct 19.

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.

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http://dx.doi.org/10.1016/j.jmb.2005.09.085DOI Listing
December 2005

Inference of human geographic origins using Alu insertion polymorphisms.

Forensic Sci Int 2005 Oct;153(2-3):117-24

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1016/j.forsciint.2004.10.017DOI Listing
October 2005

Tracking Alu evolution in New World primates.

BMC Evol Biol 2005 Oct 6;5:51. Epub 2005 Oct 6.

Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Multiscale Systems, Louisiana State University, Baton Rouge, LA 70803, USA.

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http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2148-5-51DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1266357PMC
October 2005

Modeling the amplification dynamics of human Alu retrotransposons.

PLoS Comput Biol 2005 Sep 30;1(4):e44. Epub 2005 Sep 30.

Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Microsystems, Louisiana State University, Baton Rouge, Louisiana, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.0010044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1239904PMC
September 2005

From the margins of the genome: mobile elements shape primate evolution.

Bioessays 2005 Aug;27(8):785-94

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, LA 70803, USA.

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http://dx.doi.org/10.1002/bies.20268DOI Listing
August 2005

Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages.

Nucleic Acids Res 2005 20;33(13):4040-52. Epub 2005 Jul 20.

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.

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http://dx.doi.org/10.1093/nar/gki718DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1179734PMC
August 2005

Alu retrotransposition-mediated deletion.

J Mol Biol 2005 May;348(4):791-800

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.

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http://linkinghub.elsevier.com/retrieve/pii/S002228360500220
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http://dx.doi.org/10.1016/j.jmb.2005.02.043DOI Listing
May 2005

Under the genomic radar: the stealth model of Alu amplification.

Genome Res 2005 May;15(5):655-64

Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1101/gr.3492605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088293PMC
May 2005

Alu insertion loci and platyrrhine primate phylogeny.

Mol Phylogenet Evol 2005 Apr 18;35(1):117-26. Epub 2005 Jan 18.

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.

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http://dx.doi.org/10.1016/j.ympev.2004.10.023DOI Listing
April 2005

Analysis of the human Alu Ye lineage.

BMC Evol Biol 2005 Feb 22;5:18. Epub 2005 Feb 22.

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.

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http://dx.doi.org/10.1186/1471-2148-5-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC554112PMC
February 2005