Geoffrey J Faulkner

Geoffrey J Faulkner

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Geoffrey J Faulkner

Geoffrey J Faulkner

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LINE-1 Evasion of Epigenetic Repression in Humans.

Mol Cell 2019 Aug 20;75(3):590-604.e12. Epub 2019 Jun 20.

Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10972765193039
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http://dx.doi.org/10.1016/j.molcel.2019.05.024DOI Listing
August 2019

Visualization and analysis of RNA-Seq assembly graphs.

Nucleic Acids Res 2019 08;47(14):7262-7275

Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK.

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http://dx.doi.org/10.1093/nar/gkz599DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6698738PMC
August 2019

L1 retrotransposition in the soma: a field jumping ahead.

Mob DNA 2018 7;9:22. Epub 2018 Jul 7.

3Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072 Australia.

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http://dx.doi.org/10.1186/s13100-018-0128-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6035798PMC
July 2018

Retrotransposon-induced mosaicism in the neural genome.

Open Biol 2018 07;8(7)

Mater Research Institute-University of Queensland, TRI Building, Brisbane, Queensland 4102, Australia

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http://dx.doi.org/10.1098/rsob.180074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6070720PMC
July 2018

Meeting report: mobile genetic elements and genome plasticity 2018.

Mob DNA 2018 22;9:21. Epub 2018 Jun 22.

9Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892 USA.

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http://dx.doi.org/10.1186/s13100-018-0126-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015446PMC
June 2018

L1 Mosaicism in Mammals: Extent, Effects, and Evolution.

Trends Genet 2017 11 7;33(11):802-816. Epub 2017 Aug 7.

Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK; Department of Genomic Medicine, Centre for Genomics and Oncology (Pfizer-University of Granada and Andalusian Regional Government), Health Technology Park (PTS) Granada, 18016 Granada, Spain.

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http://dx.doi.org/10.1016/j.tig.2017.07.004DOI Listing
November 2017

On the role of H3.3 in retroviral silencing.

Nature 2017 08;548(7665):E1-E3

The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland, USA.

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http://dx.doi.org/10.1038/nature23277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6258051PMC
August 2017

FANTOM5 CAGE profiles of human and mouse samples.

Authors:
Shuhei Noguchi Takahiro Arakawa Shiro Fukuda Masaaki Furuno Akira Hasegawa Fumi Hori Sachi Ishikawa-Kato Kaoru Kaida Ai Kaiho Mutsumi Kanamori-Katayama Tsugumi Kawashima Miki Kojima Atsutaka Kubosaki Ri-Ichiroh Manabe Mitsuyoshi Murata Sayaka Nagao-Sato Kenichi Nakazato Noriko Ninomiya Hiromi Nishiyori-Sueki Shohei Noma Eri Saijyo Akiko Saka Mizuho Sakai Christophe Simon Naoko Suzuki Michihira Tagami Shoko Watanabe Shigehiro Yoshida Peter Arner Richard A Axton Magda Babina J Kenneth Baillie Timothy C Barnett Anthony G Beckhouse Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher Ailsa J Carlisle Hans C Clevers Carrie A Davis Michael Detmar Taeko Dohi Albert S B Edge Matthias Edinger Anna Ehrlund Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Afsaneh Eslami Michela Fagiolini Lynsey Fairbairn Mary C Farach-Carson Geoffrey J Faulkner Carmelo Ferrai Malcolm E Fisher Lesley M Forrester Rie Fujita Jun-Ichi Furusawa Teunis B Geijtenbeek Thomas Gingeras Daniel Goldowitz Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Yuki Hasegawa Meenhard Herlyn Peter Heutink Kelly J Hitchens David A Hume Tomokatsu Ikawa Yuri Ishizu Chieko Kai Hiroshi Kawamoto Yuki I Kawamura Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura Sarah Klein S Peter Klinken Alan J Knox Soichi Kojima Haruhiko Koseki Shigeo Koyasu Weonju Lee Andreas Lennartsson Alan Mackay-Sim Niklas Mejhert Yosuke Mizuno Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Kelly J Morris Hozumi Motohashi Christine L Mummery Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Tadasuke Nozaki Soichi Ogishima Naganari Ohkura Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Robert Passier Margaret Patrikakis Ana Pombo Swati Pradhan-Bhatt Xian-Yang Qin Michael Rehli Patrizia Rizzu Sugata Roy Antti Sajantila Shimon Sakaguchi Hiroki Sato Hironori Satoh Suzana Savvi Alka Saxena Christian Schmidl Claudio Schneider Gundula G Schulze-Tanzil Anita Schwegmann Guojun Sheng Jay W Shin Daisuke Sugiyama Takaaki Sugiyama Kim M Summers Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Andru Tomoiu Hiroo Toyoda Marc van de Wetering Linda M van den Berg Roberto Verardo Dipti Vijayan Christine A Wells Louise N Winteringham Ernst Wolvetang Yoko Yamaguchi Masayuki Yamamoto Chiyo Yanagi-Mizuochi Misako Yoneda Yohei Yonekura Peter G Zhang Silvia Zucchelli Imad Abugessaisa Erik Arner Jayson Harshbarger Atsushi Kondo Timo Lassmann Marina Lizio Serkan Sahin Thierry Sengstag Jessica Severin Hisashi Shimoji Masanori Suzuki Harukazu Suzuki Jun Kawai Naoto Kondo Masayoshi Itoh Carsten O Daub Takeya Kasukawa Hideya Kawaji Piero Carninci Alistair R R Forrest Yoshihide Hayashizaki

Sci Data 2017 08 29;4:170112. Epub 2017 Aug 29.

RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1038/sdata.2017.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5574368PMC
August 2017

Retrotransposon Capture Sequencing (RC-Seq): A Targeted, High-Throughput Approach to Resolve Somatic L1 Retrotransposition in Humans.

Methods Mol Biol 2016 ;1400:47-77

Mater Research Institute,University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia.

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http://dx.doi.org/10.1007/978-1-4939-3372-3_4DOI Listing
December 2016

TET enzymes: double agents in the transposable element-host genome conflict.

Genome Biol 2016 12 20;17(1):259. Epub 2016 Dec 20.

Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia.

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http://genomebiology.biomedcentral.com/articles/10.1186/s130
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http://dx.doi.org/10.1186/s13059-016-1124-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5170891PMC
December 2016

Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant.

Am J Hum Genet 2016 05 14;98(5):830-842. Epub 2016 Apr 14.

Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2016.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863475PMC
May 2016

Transposable elements in the mammalian embryo: pioneers surviving through stealth and service.

Genome Biol 2016 May 9;17:100. Epub 2016 May 9.

Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia.

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http://dx.doi.org/10.1186/s13059-016-0965-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4862087PMC
May 2016

L1 retrotransposons and somatic mosaicism in the brain.

Annu Rev Genet 2014 14;48:1-27. Epub 2014 Jul 14.

Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba QLD 4102, Australia; email:

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http://dx.doi.org/10.1146/annurev-genet-120213-092412DOI Listing
July 2015

Ubiquitous L1 mosaicism in hippocampal neurons.

Cell 2015 Apr;161(2):228-39

Mater Research Institute - University of Queensland, TRI Building, Woolloongabba QLD 4102, Australia; Queensland Brain Institute, University of Queensland, Brisbane QLD 4072, Australia. Electronic address:

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http://www.cell.com/cell/pdf/S0092-8674(15)00313-X.pdf
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http://linkinghub.elsevier.com/retrieve/pii/S009286741500313
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http://dx.doi.org/10.1016/j.cell.2015.03.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4398972PMC
April 2015

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.

Authors:
Erik Arner Carsten O Daub Kristoffer Vitting-Seerup Robin Andersson Berit Lilje Finn Drabløs Andreas Lennartsson Michelle Rönnerblad Olga Hrydziuszko Morana Vitezic Tom C Freeman Ahmad M N Alhendi Peter Arner Richard Axton J Kenneth Baillie Anthony Beckhouse Beatrice Bodega James Briggs Frank Brombacher Margaret Davis Michael Detmar Anna Ehrlund Mitsuhiro Endoh Afsaneh Eslami Michela Fagiolini Lynsey Fairbairn Geoffrey J Faulkner Carmelo Ferrai Malcolm E Fisher Lesley Forrester Daniel Goldowitz Reto Guler Thomas Ha Mitsuko Hara Meenhard Herlyn Tomokatsu Ikawa Chieko Kai Hiroshi Kawamoto Levon M Khachigian S Peter Klinken Soichi Kojima Haruhiko Koseki Sarah Klein Niklas Mejhert Ken Miyaguchi Yosuke Mizuno Mitsuru Morimoto Kelly J Morris Christine Mummery Yutaka Nakachi Soichi Ogishima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry Ovchinnikov Robert Passier Margaret Patrikakis Ana Pombo Xian-Yang Qin Sugata Roy Hiroki Sato Suzana Savvi Alka Saxena Anita Schwegmann Daisuke Sugiyama Rolf Swoboda Hiroshi Tanaka Andru Tomoiu Louise N Winteringham Ernst Wolvetang Chiyo Yanagi-Mizuochi Misako Yoneda Susan Zabierowski Peter Zhang Imad Abugessaisa Nicolas Bertin Alexander D Diehl Shiro Fukuda Masaaki Furuno Jayson Harshbarger Akira Hasegawa Fumi Hori Sachi Ishikawa-Kato Yuri Ishizu Masayoshi Itoh Tsugumi Kawashima Miki Kojima Naoto Kondo Marina Lizio Terrence F Meehan Christopher J Mungall Mitsuyoshi Murata Hiromi Nishiyori-Sueki Serkan Sahin Sayaka Nagao-Sato Jessica Severin Michiel J L de Hoon Jun Kawai Takeya Kasukawa Timo Lassmann Harukazu Suzuki Hideya Kawaji Kim M Summers Christine Wells David A Hume Alistair R R Forrest Albin Sandelin Piero Carninci Yoshihide Hayashizaki

Science 2015 Feb 12;347(6225):1010-4. Epub 2015 Feb 12.

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http://dx.doi.org/10.1126/science.1259418DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681433PMC
February 2015

Diversity through duplication: whole-genome sequencing reveals novel gene retrocopies in the human population.

Bioessays 2014 May 25;36(5):475-81. Epub 2014 Feb 25.

Cancer Biology Program, Mater Medical Research Institute, South Brisbane, QLD, Australia.

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http://doi.wiley.com/10.1002/bies.201300181
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http://dx.doi.org/10.1002/bies.201300181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4314676PMC
May 2014

Blood from 'junk': the LTR chimeric transcript Pu.2 promotes erythropoiesis.

Mob DNA 2014 9;5:15. Epub 2014 May 9.

Mater Research Institute - University of Queensland, TRI Building, 4102 Brisbane, QLD, Australia ; School of Biomedical Sciences, University of Queensland, 4072 Brisbane, QLD, Australia.

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http://dx.doi.org/10.1186/1759-8753-5-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023170PMC
May 2014

A promoter-level mammalian expression atlas.

Authors:
Alistair R R Forrest Hideya Kawaji Michael Rehli J Kenneth Baillie Michiel J L de Hoon Vanja Haberle Timo Lassmann Ivan V Kulakovskiy Marina Lizio Masayoshi Itoh Robin Andersson Christopher J Mungall Terrence F Meehan Sebastian Schmeier Nicolas Bertin Mette Jørgensen Emmanuel Dimont Erik Arner Christian Schmidl Ulf Schaefer Yulia A Medvedeva Charles Plessy Morana Vitezic Jessica Severin Colin A Semple Yuri Ishizu Robert S Young Margherita Francescatto Intikhab Alam Davide Albanese Gabriel M Altschuler Takahiro Arakawa John A C Archer Peter Arner Magda Babina Sarah Rennie Piotr J Balwierz Anthony G Beckhouse Swati Pradhan-Bhatt Judith A Blake Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher A Maxwell Burroughs Andrea Califano Carlo V Cannistraci Daniel Carbajo Yun Chen Marco Chierici Yari Ciani Hans C Clevers Emiliano Dalla Carrie A Davis Michael Detmar Alexander D Diehl Taeko Dohi Finn Drabløs Albert S B Edge Matthias Edinger Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Michela Fagiolini Lynsey Fairbairn Hai Fang Mary C Farach-Carson Geoffrey J Faulkner Alexander V Favorov Malcolm E Fisher Martin C Frith Rie Fujita Shiro Fukuda Cesare Furlanello Masaaki Furino Jun-ichi Furusawa Teunis B Geijtenbeek Andrew P Gibson Thomas Gingeras Daniel Goldowitz Julian Gough Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Matthias Harbers Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Takehiro Hashimoto Meenhard Herlyn Kelly J Hitchens Shannan J Ho Sui Oliver M Hofmann Ilka Hoof Furni Hori Lukasz Huminiecki Kei Iida Tomokatsu Ikawa Boris R Jankovic Hui Jia Anagha Joshi Giuseppe Jurman Bogumil Kaczkowski Chieko Kai Kaoru Kaida Ai Kaiho Kazuhiro Kajiyama Mutsumi Kanamori-Katayama Artem S Kasianov Takeya Kasukawa Shintaro Katayama Sachi Kato Shuji Kawaguchi Hiroshi Kawamoto Yuki I Kawamura Tsugumi Kawashima Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura S Peter Klinken Alan J Knox Miki Kojima Soichi Kojima Naoto Kondo Haruhiko Koseki Shigeo Koyasu Sarah Krampitz Atsutaka Kubosaki Andrew T Kwon Jeroen F J Laros Weonju Lee Andreas Lennartsson Kang Li Berit Lilje Leonard Lipovich Alan Mackay-Sim Ri-ichiroh Manabe Jessica C Mar Benoit Marchand Anthony Mathelier Niklas Mejhert Alison Meynert Yosuke Mizuno David A de Lima Morais Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Efthymios Motakis Hozumi Motohashi Christine L Mummery Mitsuyoshi Murata Sayaka Nagao-Sato Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Kenichi Nakazato Erik van Nimwegen Noriko Ninomiya Hiromi Nishiyori Shohei Noma Shohei Noma Tadasuke Noazaki Soichi Ogishima Naganari Ohkura Hiroko Ohimiya Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Arnab Pain Robert Passier Margaret Patrikakis Helena Persson Silvano Piazza James G D Prendergast Owen J L Rackham Jordan A Ramilowski Mamoon Rashid Timothy Ravasi Patrizia Rizzu Marco Roncador Sugata Roy Morten B Rye Eri Saijyo Antti Sajantila Akiko Saka Shimon Sakaguchi Mizuho Sakai Hiroki Sato Suzana Savvi Alka Saxena Claudio Schneider Erik A Schultes Gundula G Schulze-Tanzil Anita Schwegmann Thierry Sengstag Guojun Sheng Hisashi Shimoji Yishai Shimoni Jay W Shin Christophe Simon Daisuke Sugiyama Takaai Sugiyama Masanori Suzuki Naoko Suzuki Rolf K Swoboda Peter A C 't Hoen Michihira Tagami Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Zuotian Tatum Mark Thompson Hiroo Toyodo Tetsuro Toyoda Elvind Valen Marc van de Wetering Linda M van den Berg Roberto Verado Dipti Vijayan Ilya E Vorontsov Wyeth W Wasserman Shoko Watanabe Christine A Wells Louise N Winteringham Ernst Wolvetang Emily J Wood Yoko Yamaguchi Masayuki Yamamoto Misako Yoneda Yohei Yonekura Shigehiro Yoshida Susan E Zabierowski Peter G Zhang Xiaobei Zhao Silvia Zucchelli Kim M Summers Harukazu Suzuki Carsten O Daub Jun Kawai Peter Heutink Winston Hide Tom C Freeman Boris Lenhard Vladimir B Bajic Martin S Taylor Vsevolod J Makeev Albin Sandelin David A Hume Piero Carninci Yoshihide Hayashizaki

Nature 2014 Mar;507(7493):462-70

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http://dx.doi.org/10.1038/nature13182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748PMC
March 2014

L1 retrotransposons, cancer stem cells and oncogenesis.

FEBS J 2014 Jan 28;281(1):63-73. Epub 2013 Nov 28.

Cancer Biology Program, Mater Medical Research Institute, South Brisbane, Australia.

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http://dx.doi.org/10.1111/febs.12601DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160015PMC
January 2014

The role of transposable elements in health and diseases of the central nervous system.

J Neurosci 2013 Nov;33(45):17577-86

National Institute on Alcohol Abuse & Alcoholism, Bethesda, Maryland 20892, Mater Medical Research Institute, South Brisbane Queensland, Australia, 4101, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, University of Texas at Austin, Waggoner Center for Alcohol & Addiction Research and the College of Pharmacy, Austin, Texas 78712, and The Salk Institute, Laboratory of Genetics, La Jolla, California 92037.

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http://www.jneurosci.org/content/33/45/17577.full.pdf
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http://www.jneurosci.org/cgi/doi/10.1523/JNEUROSCI.3369-13.2
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http://dx.doi.org/10.1523/JNEUROSCI.3369-13.2013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3818539PMC
November 2013

Retrotransposon silencing during embryogenesis: dicer cuts in LINE.

PLoS Genet 2013 Nov 7;9(11):e1003944. Epub 2013 Nov 7.

Cancer Biology Program, Mater Medical Research Institute, South Brisbane, Australia ; School of Biomedical Sciences, University of Queensland, Brisbane, Australia.

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https://dx.plos.org/10.1371/journal.pgen.1003944
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http://dx.doi.org/10.1371/journal.pgen.1003944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820789PMC
November 2013

Extensive somatic L1 retrotransposition in colorectal tumors.

Genome Res 2012 Dec 11;22(12):2328-38. Epub 2012 Sep 11.

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.1101/gr.145235.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514663PMC
December 2012

Analyses of pig genomes provide insight into porcine demography and evolution.

Authors:
Martien A M Groenen Alan L Archibald Hirohide Uenishi Christopher K Tuggle Yasuhiro Takeuchi Max F Rothschild Claire Rogel-Gaillard Chankyu Park Denis Milan Hendrik-Jan Megens Shengting Li Denis M Larkin Heebal Kim Laurent A F Frantz Mario Caccamo Hyeonju Ahn Bronwen L Aken Anna Anselmo Christian Anthon Loretta Auvil Bouabid Badaoui Craig W Beattie Christian Bendixen Daniel Berman Frank Blecha Jonas Blomberg Lars Bolund Mirte Bosse Sara Botti Zhan Bujie Megan Bystrom Boris Capitanu Denise Carvalho-Silva Patrick Chardon Celine Chen Ryan Cheng Sang-Haeng Choi William Chow Richard C Clark Christopher Clee Richard P M A Crooijmans Harry D Dawson Patrice Dehais Fioravante De Sapio Bert Dibbits Nizar Drou Zhi-Qiang Du Kellye Eversole João Fadista Susan Fairley Thomas Faraut Geoffrey J Faulkner Katie E Fowler Merete Fredholm Eric Fritz James G R Gilbert Elisabetta Giuffra Jan Gorodkin Darren K Griffin Jennifer L Harrow Alexander Hayward Kerstin Howe Zhi-Liang Hu Sean J Humphray Toby Hunt Henrik Hornshøj Jin-Tae Jeon Patric Jern Matthew Jones Jerzy Jurka Hiroyuki Kanamori Ronan Kapetanovic Jaebum Kim Jae-Hwan Kim Kyu-Won Kim Tae-Hun Kim Greger Larson Kyooyeol Lee Kyung-Tai Lee Richard Leggett Harris A Lewin Yingrui Li Wansheng Liu Jane E Loveland Yao Lu Joan K Lunney Jian Ma Ole Madsen Katherine Mann Lucy Matthews Stuart McLaren Takeya Morozumi Michael P Murtaugh Jitendra Narayan Dinh Truong Nguyen Peixiang Ni Song-Jung Oh Suneel Onteru Frank Panitz Eung-Woo Park Hong-Seog Park Geraldine Pascal Yogesh Paudel Miguel Perez-Enciso Ricardo Ramirez-Gonzalez James M Reecy Sandra Rodriguez-Zas Gary A Rohrer Lauretta Rund Yongming Sang Kyle Schachtschneider Joshua G Schraiber John Schwartz Linda Scobie Carol Scott Stephen Searle Bertrand Servin Bruce R Southey Goran Sperber Peter Stadler Jonathan V Sweedler Hakim Tafer Bo Thomsen Rashmi Wali Jian Wang Jun Wang Simon White Xun Xu Martine Yerle Guojie Zhang Jianguo Zhang Jie Zhang Shuhong Zhao Jane Rogers Carol Churcher Lawrence B Schook

Nature 2012 Nov;491(7424):393-8

Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.

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http://www.umass.edu/vetimm/docs/Groenen_etal_2012.pdf
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http://www.nature.com/doifinder/10.1038/nature11622
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http://dx.doi.org/10.1038/nature11622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566564PMC
November 2012

Is somatic retrotransposition a parasitic or symbiotic phenomenon?

Mob Genet Elements 2011 Nov;1(4):279-282

Division of Genetics and Genomics; The Roslin Institute and Royal (Dick) School of Veterinary Studies; University of Edinburgh; Easter Bush, UK.

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http://www.tandfonline.com/doi/abs/10.4161/mge.18422
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http://dx.doi.org/10.4161/mge.18422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337137PMC
November 2011

Somatic retrotransposition alters the genetic landscape of the human brain.

Nature 2011 Oct 30;479(7374):534-7. Epub 2011 Oct 30.

Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK.

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http://dx.doi.org/10.1038/nature10531DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3224101PMC
October 2011

Retrotransposons: mobile and mutagenic from conception to death.

FEBS Lett 2011 Jun 6;585(11):1589-94. Epub 2011 Apr 6.

Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, UK.

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http://doi.wiley.com/10.1016/j.febslet.2011.03.061
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http://dx.doi.org/10.1016/j.febslet.2011.03.061DOI Listing
June 2011

A global view of genomic information--moving beyond the gene and the master regulator.

Trends Genet 2010 Jan 26;26(1):21-8. Epub 2009 Nov 26.

Institute for Molecular Bioscience, The University of Queensland, St Lucia, 4072 QLD, Australia.

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http://linkinghub.elsevier.com/retrieve/pii/S016895250900230
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http://dx.doi.org/10.1016/j.tig.2009.11.002DOI Listing
January 2010

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite.

Bioinformatics 2009 Oct 15;25(19):2613-4. Epub 2009 Jul 15.

Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btp438DOI Listing
October 2009

RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data.

Bioinformatics 2009 Oct 30;25(19):2615-6. Epub 2009 Jul 30.

Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St. Lucia 4072, Australia.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btp459DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752615PMC
October 2009

Altruistic functions for selfish DNA.

Cell Cycle 2009 Sep;8(18):2895-900

Roslin Institute, University of Edinburgh, Roslin, Scotland, UK.

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http://www.tandfonline.com/doi/abs/10.4161/cc.8.18.9536
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http://dx.doi.org/10.4161/cc.8.18.9536DOI Listing
September 2009

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

Authors:
Harukazu Suzuki Alistair R R Forrest Erik van Nimwegen Carsten O Daub Piotr J Balwierz Katharine M Irvine Timo Lassmann Timothy Ravasi Yuki Hasegawa Michiel J L de Hoon Shintaro Katayama Kate Schroder Piero Carninci Yasuhiro Tomaru Mutsumi Kanamori-Katayama Atsutaka Kubosaki Altuna Akalin Yoshinari Ando Erik Arner Maki Asada Hiroshi Asahara Timothy Bailey Vladimir B Bajic Denis Bauer Anthony G Beckhouse Nicolas Bertin Johan Björkegren Frank Brombacher Erika Bulger Alistair M Chalk Joe Chiba Nicole Cloonan Adam Dawe Josee Dostie Pär G Engström Magbubah Essack Geoffrey J Faulkner J Lynn Fink David Fredman Ko Fujimori Masaaki Furuno Takashi Gojobori Julian Gough Sean M Grimmond Mika Gustafsson Megumi Hashimoto Takehiro Hashimoto Mariko Hatakeyama Susanne Heinzel Winston Hide Oliver Hofmann Michael Hörnquist Lukasz Huminiecki Kazuho Ikeo Naoko Imamoto Satoshi Inoue Yusuke Inoue Ryoko Ishihara Takao Iwayanagi Anders Jacobsen Mandeep Kaur Hideya Kawaji Markus C Kerr Ryuichiro Kimura Syuhei Kimura Yasumasa Kimura Hiroaki Kitano Hisashi Koga Toshio Kojima Shinji Kondo Takeshi Konno Anders Krogh Adele Kruger Ajit Kumar Boris Lenhard Andreas Lennartsson Morten Lindow Marina Lizio Cameron Macpherson Norihiro Maeda Christopher A Maher Monique Maqungo Jessica Mar Nicholas A Matigian Hideo Matsuda John S Mattick Stuart Meier Sei Miyamoto Etsuko Miyamoto-Sato Kazuhiko Nakabayashi Yutaka Nakachi Mika Nakano Sanne Nygaard Toshitsugu Okayama Yasushi Okazaki Haruka Okuda-Yabukami Valerio Orlando Jun Otomo Mikhail Pachkov Nikolai Petrovsky Charles Plessy John Quackenbush Aleksandar Radovanovic Michael Rehli Rintaro Saito Albin Sandelin Sebastian Schmeier Christian Schönbach Ariel S Schwartz Colin A Semple Miho Sera Jessica Severin Katsuhiko Shirahige Cas Simons George St Laurent Masanori Suzuki Takahiro Suzuki Matthew J Sweet Ryan J Taft Shizu Takeda Yoichi Takenaka Kai Tan Martin S Taylor Rohan D Teasdale Jesper Tegnér Sarah Teichmann Eivind Valen Claes Wahlestedt Kazunori Waki Andrew Waterhouse Christine A Wells Ole Winther Linda Wu Kazumi Yamaguchi Hiroshi Yanagawa Jun Yasuda Mihaela Zavolan David A Hume Takahiro Arakawa Shiro Fukuda Kengo Imamura Chikatoshi Kai Ai Kaiho Tsugumi Kawashima Chika Kawazu Yayoi Kitazume Miki Kojima Hisashi Miura Kayoko Murakami Mitsuyoshi Murata Noriko Ninomiya Hiromi Nishiyori Shohei Noma Chihiro Ogawa Takuma Sano Christophe Simon Michihira Tagami Yukari Takahashi Jun Kawai Yoshihide Hayashizaki

Nat Genet 2009 May 19;41(5):553-62. Epub 2009 Apr 19.

RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan.

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http://dx.doi.org/10.1038/ng.375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711855PMC
May 2009

A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE.

Genomics 2008 Mar;91(3):281-8

The Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia.

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http://dx.doi.org/10.1016/j.ygeno.2007.11.003DOI Listing
March 2008

The expression of Clcn7 and Ostm1 in osteoclasts is coregulated by microphthalmia transcription factor.

J Biol Chem 2007 Jan 14;282(3):1891-904. Epub 2006 Nov 14.

Institute for Molecular Biosciences, the University of Queensland, St. Lucia, Queensland 4072, Australia.

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http://dx.doi.org/10.1074/jbc.M608572200DOI Listing
January 2007

Genetic control of the innate immune response.

BMC Immunol 2003 Jun 26;4. Epub 2003 Jun 26.

Institute for Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.

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http://dx.doi.org/10.1186/1471-2172-4-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC194878PMC
June 2003