Publications by authors named "Thomas Eickbush"

46Publications

Integrated cytogenetics and genomics analysis of transposable elements in the Nile tilapia, Oreochromis niloticus.

Mol Genet Genomics 2016 Jun 9;291(3):1219-25. Epub 2016 Feb 9.

Morphology Department, Institute of Biosciences, UNESP, Sao Paulo State University, 18618-689, Botucatu, SP, Brazil.

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June 2016

Integration, Regulation, and Long-Term Stability of R2 Retrotransposons.

Microbiol Spectr 2015 Apr;3(2):MDNA3-0011-2014

Department of Biology, University of Rochester, Rochester, NY 14627.

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April 2015

Identification of RNA binding motifs in the R2 retrotransposon-encoded reverse transcriptase.

Nucleic Acids Res 2014 Jul 23;42(13):8405-15. Epub 2014 Jun 23.

Department of Biology, University of Rochester, Rochester, NY 14627, USA

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July 2014

Evolution of the R2 retrotransposon ribozyme and its self-cleavage site.

PLoS One 2013 16;8(9):e66441. Epub 2013 Sep 16.

Department of Biology, University of Rochester, Rochester, New York, United States of America.

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May 2014

In and out of the rRNA genes: characterization of Pokey elements in the sequenced Daphnia genome.

Mob DNA 2013 Sep 23;4(1):20. Epub 2013 Sep 23.

Department of Biology, University of Rochester, Rochester, NY 14627, USA.

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September 2013

A population genetic model for the maintenance of R2 retrotransposons in rRNA gene loci.

PLoS Genet 2013 10;9(1):e1003179. Epub 2013 Jan 10.

Department of Biology, University of Rochester, Rochester, New York, United States of America.

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May 2013

Y chromosome mediates ribosomal DNA silencing and modulates the chromatin state in Drosophila.

Proc Natl Acad Sci U S A 2012 Jun 4;109(25):9941-6. Epub 2012 Jun 4.

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.

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June 2012

R2 and R2/R1 hybrid non-autonomous retrotransposons derived by internal deletions of full-length elements.

Mob DNA 2012 May 23;3(1):10. Epub 2012 May 23.

Department of Biology, University of Rochester, Rochester, NY, 14627, USA.

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May 2012

Heterochromatin formation promotes longevity and represses ribosomal RNA synthesis.

PLoS Genet 2012 Jan 26;8(1):e1002473. Epub 2012 Jan 26.

Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York, USA.

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January 2012

Retrotransposition of R2 elements in somatic nuclei during the early development of Drosophila.

Mob DNA 2011 Sep 29;2(1):11. Epub 2011 Sep 29.

Department of Biology, University of Rochester, Rochester, NY, USA.

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September 2011

The R2 retrotransposon RNA families.

RNA Biol 2011 Sep-Oct;8(5):714-8. Epub 2011 Jul 7.

Department of Chemistry, University of Rochester, Rochester, NY, USA.

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January 2013

The reverse transcriptase encoded by the non-LTR retrotransposon R2 is as error-prone as that encoded by HIV-1.

J Mol Biol 2011 Apr 12;407(5):661-72. Epub 2011 Feb 12.

Department of Biology, University of Rochester, Rochester, NY 14627-0211, USA.

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April 2011

R2 retrotransposons encode a self-cleaving ribozyme for processing from an rRNA cotranscript.

Mol Cell Biol 2010 Jul 26;30(13):3142-50. Epub 2010 Apr 26.

Department of Biology, University of Rochester, Rochester, NY 14627, USA.

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July 2010

Welcome to mobile DNA.

Mob DNA 2010 Jan 25;1(1). Epub 2010 Jan 25.

Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

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January 2010

Origin of nascent lineages and the mechanisms used to prime second-strand DNA synthesis in the R1 and R2 retrotransposons of Drosophila.

Genome Biol 2009 5;10(5):R49. Epub 2009 May 5.

Biology Department, University of Rochester, Rochester NY 14627-0211, USA.

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August 2009

The pattern of R2 retrotransposon activity in natural populations of Drosophila simulans reflects the dynamic nature of the rDNA locus.

PLoS Genet 2009 Feb 20;5(2):e1000386. Epub 2009 Feb 20.

Department of Biology, University of Rochester, Rochester, New York, United States of America.

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February 2009

Role of recombination in the long-term retention of transposable elements in rRNA gene loci.

Genetics 2008 Nov 14;180(3):1617-26. Epub 2008 Sep 14.

Department of Biology, University of Rochester, Rochester, New York 14627-0211, USA.

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November 2008

Epigenetic regulation of retrotransposons within the nucleolus of Drosophila.

Mol Cell Biol 2008 Oct 4;28(20):6452-61. Epub 2008 Aug 4.

Department of Biology, University of Rochester, Rochester, NY 14627, USA.

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October 2008

The diversity of retrotransposons and the properties of their reverse transcriptases.

Virus Res 2008 Jun 7;134(1-2):221-34. Epub 2008 Feb 7.

Department of Biology, University of Rochester, Rochester, NY 14627, USA.

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June 2008

Rapid R2 retrotransposition leads to the loss of previously inserted copies via large deletions of the rDNA locus.

Mol Biol Evol 2008 Jan 13;25(1):229-37. Epub 2007 Nov 13.

Department of Biology, University of Rochester, USA.

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January 2008

Evolution of genes and genomes on the Drosophila phylogeny.

Authors:
Andrew G Clark Michael B Eisen Douglas R Smith Casey M Bergman Brian Oliver Therese A Markow Thomas C Kaufman Manolis Kellis William Gelbart Venky N Iyer Daniel A Pollard Timothy B Sackton Amanda M Larracuente Nadia D Singh Jose P Abad Dawn N Abt Boris Adryan Montserrat Aguade Hiroshi Akashi Wyatt W Anderson Charles F Aquadro David H Ardell Roman Arguello Carlo G Artieri Daniel A Barbash Daniel Barker Paolo Barsanti Phil Batterham Serafim Batzoglou Dave Begun Arjun Bhutkar Enrico Blanco Stephanie A Bosak Robert K Bradley Adrianne D Brand Michael R Brent Angela N Brooks Randall H Brown Roger K Butlin Corrado Caggese Brian R Calvi A Bernardo de Carvalho Anat Caspi Sergio Castrezana Susan E Celniker Jean L Chang Charles Chapple Sourav Chatterji Asif Chinwalla Alberto Civetta Sandra W Clifton Josep M Comeron James C Costello Jerry A Coyne Jennifer Daub Robert G David Arthur L Delcher Kim Delehaunty Chuong B Do Heather Ebling Kevin Edwards Thomas Eickbush Jay D Evans Alan Filipski Sven Findeiss Eva Freyhult Lucinda Fulton Robert Fulton Ana C L Garcia Anastasia Gardiner David A Garfield Barry E Garvin Greg Gibson Don Gilbert Sante Gnerre Jennifer Godfrey Robert Good Valer Gotea Brenton Gravely Anthony J Greenberg Sam Griffiths-Jones Samuel Gross Roderic Guigo Erik A Gustafson Wilfried Haerty Matthew W Hahn Daniel L Halligan Aaron L Halpern Gillian M Halter Mira V Han Andreas Heger LaDeana Hillier Angie S Hinrichs Ian Holmes Roger A Hoskins Melissa J Hubisz Dan Hultmark Melanie A Huntley David B Jaffe Santosh Jagadeeshan William R Jeck Justin Johnson Corbin D Jones William C Jordan Gary H Karpen Eiko Kataoka Peter D Keightley Pouya Kheradpour Ewen F Kirkness Leonardo B Koerich Karsten Kristiansen Dave Kudrna Rob J Kulathinal Sudhir Kumar Roberta Kwok Eric Lander Charles H Langley Richard Lapoint Brian P Lazzaro So-Jeong Lee Lisa Levesque Ruiqiang Li Chiao-Feng Lin Michael F Lin Kerstin Lindblad-Toh Ana Llopart Manyuan Long Lloyd Low Elena Lozovsky Jian Lu Meizhong Luo Carlos A Machado Wojciech Makalowski Mar Marzo Muneo Matsuda Luciano Matzkin Bryant McAllister Carolyn S McBride Brendan McKernan Kevin McKernan Maria Mendez-Lago Patrick Minx Michael U Mollenhauer Kristi Montooth Stephen M Mount Xu Mu Eugene Myers Barbara Negre Stuart Newfeld Rasmus Nielsen Mohamed A F Noor Patrick O'Grady Lior Pachter Montserrat Papaceit Matthew J Parisi Michael Parisi Leopold Parts Jakob S Pedersen Graziano Pesole Adam M Phillippy Chris P Ponting Mihai Pop Damiano Porcelli Jeffrey R Powell Sonja Prohaska Kim Pruitt Marta Puig Hadi Quesneville Kristipati Ravi Ram David Rand Matthew D Rasmussen Laura K Reed Robert Reenan Amy Reily Karin A Remington Tania T Rieger Michael G Ritchie Charles Robin Yu-Hui Rogers Claudia Rohde Julio Rozas Marc J Rubenfield Alfredo Ruiz Susan Russo Steven L Salzberg Alejandro Sanchez-Gracia David J Saranga Hajime Sato Stephen W Schaeffer Michael C Schatz Todd Schlenke Russell Schwartz Carmen Segarra Rama S Singh Laura Sirot Marina Sirota Nicholas B Sisneros Chris D Smith Temple F Smith John Spieth Deborah E Stage Alexander Stark Wolfgang Stephan Robert L Strausberg Sebastian Strempel David Sturgill Granger Sutton Granger G Sutton Wei Tao Sarah Teichmann Yoshiko N Tobari Yoshihiko Tomimura Jason M Tsolas Vera L S Valente Eli Venter J Craig Venter Saverio Vicario Filipe G Vieira Albert J Vilella Alfredo Villasante Brian Walenz Jun Wang Marvin Wasserman Thomas Watts Derek Wilson Richard K Wilson Rod A Wing Mariana F Wolfner Alex Wong Gane Ka-Shu Wong Chung-I Wu Gabriel Wu Daisuke Yamamoto Hsiao-Pei Yang Shiaw-Pyng Yang James A Yorke Kiyohito Yoshida Evgeny Zdobnov Peili Zhang Yu Zhang Aleksey V Zimin Jennifer Baldwin Amr Abdouelleil Jamal Abdulkadir Adal Abebe Brikti Abera Justin Abreu St Christophe Acer Lynne Aftuck Allen Alexander Peter An Erica Anderson Scott Anderson Harindra Arachi Marc Azer Pasang Bachantsang Andrew Barry Tashi Bayul Aaron Berlin Daniel Bessette Toby Bloom Jason Blye Leonid Boguslavskiy Claude Bonnet Boris Boukhgalter Imane Bourzgui Adam Brown Patrick Cahill Sheridon Channer Yama Cheshatsang Lisa Chuda Mieke Citroen Alville Collymore Patrick Cooke Maura Costello Katie D'Aco Riza Daza Georgius De Haan Stuart DeGray Christina DeMaso Norbu Dhargay Kimberly Dooley Erin Dooley Missole Doricent Passang Dorje Kunsang Dorjee Alan Dupes Richard Elong Jill Falk Abderrahim Farina Susan Faro Diallo Ferguson Sheila Fisher Chelsea D Foley Alicia Franke Dennis Friedrich Loryn Gadbois Gary Gearin Christina R Gearin Georgia Giannoukos Tina Goode Joseph Graham Edward Grandbois Sharleen Grewal Kunsang Gyaltsen Nabil Hafez Birhane Hagos Jennifer Hall Charlotte Henson Andrew Hollinger Tracey Honan Monika D Huard Leanne Hughes Brian Hurhula M Erii Husby Asha Kamat Ben Kanga Seva Kashin Dmitry Khazanovich Peter Kisner Krista Lance Marcia Lara William Lee Niall Lennon Frances Letendre Rosie LeVine Alex Lipovsky Xiaohong Liu Jinlei Liu Shangtao Liu Tashi Lokyitsang Yeshi Lokyitsang Rakela Lubonja Annie Lui Pen MacDonald Vasilia Magnisalis Kebede Maru Charles Matthews William McCusker Susan McDonough Teena Mehta James Meldrim Louis Meneus Oana Mihai Atanas Mihalev Tanya Mihova Rachel Mittelman Valentine Mlenga Anna Montmayeur Leonidas Mulrain Adam Navidi Jerome Naylor Tamrat Negash Thu Nguyen Nga Nguyen Robert Nicol Choe Norbu Nyima Norbu Nathaniel Novod Barry O'Neill Sahal Osman Eva Markiewicz Otero L Oyono Christopher Patti Pema Phunkhang Fritz Pierre Margaret Priest Sujaa Raghuraman Filip Rege Rebecca Reyes Cecil Rise Peter Rogov Keenan Ross Elizabeth Ryan Sampath Settipalli Terry Shea Ngawang Sherpa Lu Shi Diana Shih Todd Sparrow Jessica Spaulding John Stalker Nicole Stange-Thomann Sharon Stavropoulos Catherine Stone Christopher Strader Senait Tesfaye Talene Thomson Yama Thoulutsang Dawa Thoulutsang Kerri Topham Ira Topping Tsamla Tsamla Helen Vassiliev Andy Vo Tsering Wangchuk Tsering Wangdi Michael Weiand Jane Wilkinson Adam Wilson Shailendra Yadav Geneva Young Qing Yu Lisa Zembek Danni Zhong Andrew Zimmer Zac Zwirko David B Jaffe Pablo Alvarez Will Brockman Jonathan Butler CheeWhye Chin Sante Gnerre Manfred Grabherr Michael Kleber Evan Mauceli Iain MacCallum

Nature 2007 Nov;450(7167):203-18

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.

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November 2007

Sequence variation within the rRNA gene loci of 12 Drosophila species.

Genome Res 2007 Dec 7;17(12):1888-97. Epub 2007 Nov 7.

University of Rochester, Department of Biology, Rochester, New York 14627, USA.

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December 2007

DNA-directed DNA polymerase and strand displacement activity of the reverse transcriptase encoded by the R2 retrotransposon.

J Mol Biol 2007 Nov 20;374(2):322-33. Epub 2007 Sep 20.

Department of Biology, University of Rochester, Rochester, NY 14627-0211, USA.

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November 2007

Finely orchestrated movements: evolution of the ribosomal RNA genes.

Genetics 2007 Feb;175(2):477-85

Department of Biology, University of Rochester, Rochester, New York 14627, USA.

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February 2007

RNA from the 5' end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site.

Proc Natl Acad Sci U S A 2006 Nov 14;103(47):17602-7. Epub 2006 Nov 14.

Department of Biology, University of Rochester, Rochester, NY 14627-0211, USA.

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November 2006

Chromatin structure and transcription of the R1- and R2-inserted rRNA genes of Drosophila melanogaster.

Mol Cell Biol 2006 Dec 25;26(23):8781-90. Epub 2006 Sep 25.

Department of Biology, University of Rochester, Rochester, NY 14627, USA.

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December 2006

Role of the Bombyx mori R2 element N-terminal domain in the target-primed reverse transcription (TPRT) reaction.

Nucleic Acids Res 2005 10;33(20):6461-8. Epub 2005 Nov 10.

Department of Biology, University of Rochester, Rochester, NY 14627-0211, USA.

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December 2005

Monitoring the mode and tempo of concerted evolution in the Drosophila melanogaster rDNA locus.

Genetics 2005 Dec 2;171(4):1837-46. Epub 2005 Sep 2.

Department of Biology, University of Rochester, Rochester, NY 14627-0211, USA.

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December 2005

Characterization of active R2 retrotransposition in the rDNA locus of Drosophila simulans.

Genetics 2005 May 21;170(1):195-205. Epub 2005 Mar 21.

Department of Biology, University of Rochester, New York 14627, USA.

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May 2005

Footprint of the retrotransposon R2Bm protein on its target site before and after cleavage.

J Mol Biol 2004 Mar;336(5):1035-45

Department of Biology, University of Rochester, Hutchinson Hall 334, Rochester, NY 14627-0211, USA.

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March 2004

End-to-end template jumping by the reverse transcriptase encoded by the R2 retrotransposon.

J Biol Chem 2004 Apr 28;279(15):14945-53. Epub 2004 Jan 28.

Department of Biology, University of Rochester, Rochester, New York 14627, USA.

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April 2004

R1 and R2 retrotransposition and deletion in the rDNA loci on the X and Y chromosomes of Drosophila melanogaster.

Genetics 2003 Oct;165(2):675-85

Department of Biology, University of Rochester, Rochester, New York 14627, USA.

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October 2003

R5 retrotransposons insert into a family of infrequently transcribed 28S rRNA genes of planaria.

Mol Biol Evol 2003 Aug 30;20(8):1260-70. Epub 2003 May 30.

Department of Biology, University of Rochester, USA.

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August 2003

Transcription of endogenous and exogenous R2 elements in the rRNA gene locus of Drosophila melanogaster.

Mol Cell Biol 2003 Jun;23(11):3825-36

Department of Biology, University of Rochester, Rochester, New York 146270-0211, USA.

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June 2003

R2 retrotransposition on assembled nucleosomes depends on the translational position of the target site.

EMBO J 2002 Dec;21(24):6853-64

University of Rochester, Department of Biology, Rochester, NY 14627, USA.

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December 2002

Fruit flies and humans respond differently to retrotransposons.

Curr Opin Genet Dev 2002 Dec;12(6):669-74

Department of Biology, University of Rochester, Rochester, New York 14627, USA.

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December 2002

Rates of R1 and R2 retrotransposition and elimination from the rDNA locus of Drosophila melanogaster.

Genetics 2002 Oct;162(2):799-811

Department of Biology, University of Rochester, New York 14627, USA.

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October 2002

High processivity of the reverse transcriptase from a non-long terminal repeat retrotransposon.

J Biol Chem 2002 Sep 5;277(38):34836-45. Epub 2002 Jul 5.

Department of Biology, University of Rochester, Rochester, New York 14627-0211, USA.

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September 2002

Repair by retrotransposition.

Nat Genet 2002 Jun 13;31(2):126-7. Epub 2002 May 13.

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June 2002

Ancient lineages of non-LTR retrotransposons in the primitive eukaryote, Giardia lamblia.

Mol Biol Evol 2002 May;19(5):619-30

Department of Biology, University of Rochester, Rochester, NY 14627, USA.

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May 2002

The reverse transcriptase of the R2 non-LTR retrotransposon: continuous synthesis of cDNA on non-continuous RNA templates.

J Mol Biol 2002 Feb;316(3):459-73

Department of Biology, University of Rochester, Rochester, NY 4627-0211, USA.

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February 2002