Publications by authors named "Wojciech Makalowski"

77Publications

GenoTypeMapper: graphical genotyping on genetic and sequence-based maps.

Plant Methods 2020 10;16:123. Epub 2020 Sep 10.

Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany.

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September 2020

The multicomparative 2-n-way genome suite.

Genome Res 2020 Oct 29;30(10):1508-1516. Epub 2020 Jul 29.

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

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October 2020

RAB5A and TRAPPC6B are novel targets for Shiga toxin 2a inactivation in kidney epithelial cells.

Sci Rep 2020 03 18;10(1):4945. Epub 2020 Mar 18.

Institute for Hygiene and National Consulting Laboratory for Hemolytic Uremic Syndrome (HUS), University of Münster, D-48149, Münster, Germany.

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March 2020

Enhancer occlusion transcripts regulate the activity of human enhancer domains via transcriptional interference: a computational perspective.

Nucleic Acids Res 2020 04;48(7):3435-3454

Institute of Experimental Pathology, Centre for Molecular Biology of Inflammation (ZMBE), University of Münster, Von-Esmarch-Strasse 56, D-48149 Münster, Germany.

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April 2020

Emergence and Evolution of ERM Proteins and Merlin in Metazoans.

Genome Biol Evol 2020 01;12(1):3710-3724

Institue of Bioinformatics, University of Muenster, Germany.

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January 2020

An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo.

Sci Rep 2019 09 16;9(1):13356. Epub 2019 Sep 16.

Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Ernst-Heydemann Str. 8, 18057, Rostock, Germany.

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September 2019

Bioinformatics of nanopore sequencing.

J Hum Genet 2020 Jan 26;65(1):61-67. Epub 2019 Aug 26.

Institute of Bioinformatics, Faculty of Medicine, University of Münster, 48149, Münster, Germany.

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January 2020

Transposable Elements: Classification, Identification, and Their Use As a Tool For Comparative Genomics.

Methods Mol Biol 2019 ;1910:177-207

Institute of Anthropology, Adam Mickiewicz University, Poznań, Poland.

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January 2020

Transposable elements significantly contributed to the core promoters in the human genome.

Sci China Life Sci 2019 Apr 19;62(4):489-497. Epub 2019 Mar 19.

Institute of Bioinformatics, Faculty of Medicine, University of Münster, 48149, Münster, Germany.

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April 2019

NanoPipe-a web server for nanopore MinION sequencing data analysis.

Gigascience 2019 02;8(2)

Institue of Bioinformatics, University of Muenster, Niels-Stensen-Strasse 14, Muenster, 48149, Germany.

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February 2019

Life cycle adapted upstream open reading frames (uORFs) in Trypanosoma congolense: A post-transcriptional approach to accurate gene regulation.

PLoS One 2018 9;13(8):e0201461. Epub 2018 Aug 9.

University of Münster, Faculty of Medicine, Institute of Bioinformatics, Münster, Germany.

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January 2019

Mutational Intratumor Heterogeneity is a Complex and Early Event in the Development of Adult T-cell Leukemia/Lymphoma.

Neoplasia 2018 09 19;20(9):883-893. Epub 2018 Jul 19.

Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan; Department of Advanced Medical Innovation St. Marianna University Graduate School of Medicine, Kanagawa, Japan. Electronic address:

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September 2018

Nanopore sequencing of drug-resistance-associated genes in malaria parasites, Plasmodium falciparum.

Sci Rep 2018 05 29;8(1):8286. Epub 2018 May 29.

Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.

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May 2018

Environmental adaptation of and at genome level as seen by comparative genomic analysis.

Int J Biol Sci 2018 12;14(3):306-320. Epub 2018 Feb 12.

Institute of Bioinformatics, University Münster, Niels-Stensen Strasse 14, Münster 48149, Germany.

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April 2019

Transcriptional interference by small transcripts in proximal promoter regions.

Nucleic Acids Res 2018 02;46(3):1069-1088

Institute of Experimental Pathology (ZMBE), Centre for Molecular Biology of Inflammation, University of Muenster, Von-Esmarch-Strasse 56, D-48149 Muenster, Germany.

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February 2018

The emerging picture of the mitochondrial protein import complexes of Amoebozoa supergroup.

BMC Genomics 2017 12 29;18(1):997. Epub 2017 Dec 29.

Laboratory of Bioenergetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.

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December 2017

Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer.

DNA Res 2017 Dec;24(6):585-596

Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.

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December 2017

Inferring clonal structure in HTLV-1-infected individuals: towards bridging the gap between analysis and visualization.

Hum Genomics 2017 07 11;11(1):15. Epub 2017 Jul 11.

Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa-shi, Chiba, Japan.

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July 2017

Serotyping dengue virus with isothermal amplification and a portable sequencer.

Sci Rep 2017 06 14;7(1):3510. Epub 2017 Jun 14.

Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.

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June 2017

Conservation of the Exon-Intron Structure of Long Intergenic Non-Coding RNA Genes in Eutherian Mammals.

Life (Basel) 2016 Jul 15;6(3). Epub 2016 Jul 15.

Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

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July 2016

Protein import complexes in the mitochondrial outer membrane of Amoebozoa representatives.

BMC Genomics 2016 Feb 6;17:99. Epub 2016 Feb 6.

Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Niels Stensen Strasse 14, 48149, Muenster, Germany.

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February 2016

TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability.

Sci Rep 2015 Aug 26;5:13456. Epub 2015 Aug 26.

Westfälische Wilhelms-Universität Münster, ZMBE, Institute of Cell Biology, Stem Cell Biology and Regeneration Group, Von-Esmarch-Str. 56, 48149 Münster, Germany.

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August 2015

The TOM Complex of Amoebozoans: the Cases of the Amoeba Acanthamoeba castellanii and the Slime Mold Dictyostelium discoideum.

Protist 2015 Jul 28;166(3):349-62. Epub 2015 May 28.

Adam Mickiewicz University, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Bioenergetics, Poznań, Poland.

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July 2015

DB-AT: a 2015 update to the Full-parasites database brings a multitude of new transcriptomic data for apicomplexan parasites.

Nucleic Acids Res 2015 Jan 20;43(Database issue):D631-6. Epub 2014 Nov 20.

Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido 001-0020, Japan Global Station for Zoonosis Control, GI-CoRE, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido 001-0020, Japan

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January 2015

Structural models for the design of novel antiviral agents against Greek Goat Encephalitis.

PeerJ 2014 6;2:e664. Epub 2014 Nov 6.

Computational Biology & Medicine Group, Biomedical Research Foundation, Academy of Athens , Athens , Greece.

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November 2014

Differences in embryo quality are associated with differences in oocyte composition: a proteomic study in inbred mice.

Proteomics 2015 Feb 3;15(4):675-87. Epub 2015 Jan 3.

Max Planck Institute for Molecular Biomedicine, Münster, Germany; Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany.

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February 2015

GPAC-genome presence/absence compiler: a web application to comparatively visualize multiple genome-level changes.

Mol Biol Evol 2015 Jan 25;32(1):275-86. Epub 2014 Sep 25.

Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany

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January 2015

Amoebozoa possess lineage-specific globin gene repertoires gained by individual horizontal gene transfers.

Int J Biol Sci 2014 19;10(7):689-701. Epub 2014 Jun 19.

1. Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Niels Stensen Str. 14, 48149 Muenster, Germany ; 3. Department of Medical Genomic Sciences, University of Tokyo, Tokyo, Japan.

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March 2015

Molecular dynamics simulations through GPU video games technologies.

J Mol Biochem 2014;3(2):64-71. Epub 2014 Jun 30.

Computational Biology & Medicine Group, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece.

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June 2014

Characterization of the mitochondrial genome of Rousettus leschenaulti.

Mitochondrial DNA 2014 Dec 2;25(6):443-4. Epub 2013 Jul 2.

Laboratory of Bioinformatics, Adam Mickiewicz University , Poznan , Poland .

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December 2014

Retrophylogenomics place tarsiers on the evolutionary branch of anthropoids.

Sci Rep 2013 ;3:1756

Institute of Experimental Pathology, University of Münster, 48149 Münster, Germany.

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February 2014

Surprisingly high number of Twintrons in vertebrates.

Biol Direct 2013 Jan 28;8. Epub 2013 Jan 28.

Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Niels Stensen Strasse 14, Muenster 48149, Germany.

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January 2013

Comparative genomics of neuroglobin reveals its early origins.

PLoS One 2012 25;7(10):e47972. Epub 2012 Oct 25.

Faculty of Medicine, Institute of Bioinformatics, University of Muenster, Muenster, Germany.

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May 2013

"Orphan" retrogenes in the human genome.

Mol Biol Evol 2013 Feb 12;30(2):384-96. Epub 2012 Oct 12.

Laboratory of Bionformatics, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland.

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February 2013

Transposable elements and their identification.

Methods Mol Biol 2012 ;855:337-59

Institute of Bioinformatics, University of Muenster, Muenster, Germany.

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July 2012

U12-type spliceosomal introns of Insecta.

Int J Biol Sci 2012 17;8(3):344-52. Epub 2012 Feb 17.

Institute of Bioinformatics, University of Muenster, Muenster, Germany.

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July 2012

Phylogenetic analysis of mitochondrial outer membrane β-barrel channels.

Genome Biol Evol 2012 8;4(2):110-25. Epub 2011 Dec 8.

Laboratory of Bioenergetics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland.

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September 2012

Phylogenetic analysis reveals wide distribution of globin X.

Biol Direct 2011 Oct 17;6:54. Epub 2011 Oct 17.

Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Niels Stensen Str, 14, 48149 Muenster, Germany.

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October 2011

A novel web-based TinT application and the chronology of the Primate Alu retroposon activity.

BMC Evol Biol 2010 Dec 2;10:376. Epub 2010 Dec 2.

Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str, 56, 48149 Münster, Germany.

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December 2010

Origin of the 1918 pandemic H1N1 influenza A virus as studied by codon usage patterns and phylogenetic analysis.

RNA 2011 Jan 10;17(1):64-73. Epub 2010 Nov 10.

Institute of Molecular Virology (IMV), Centre of Molecular Biology of Inflammation (ZMBE), University of Münster, 48149 Münster, Germany.

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January 2011

Evolutionary dynamics of U12-type spliceosomal introns.

BMC Evol Biol 2010 Feb 17;10:47. Epub 2010 Feb 17.

Institute of Bioinformatics, University of Muenster, Muenster, Germany.

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February 2010

Genome evolution.

Adv Bioinformatics 2010 21;2010:643701. Epub 2011 Jul 21.

Laboratory of Bioinformatics, Faculty of Biology, A. Mickiewicz University, 61-614 Poznań, Poland.

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November 2011

TEclass--a tool for automated classification of unknown eukaryotic transposable elements.

Bioinformatics 2009 May 5;25(10):1329-30. Epub 2009 Apr 5.

Katholieke Universiteit Leuven, Department of Biology, Laboratory of Aquatic Ecology and Evolutionary Biology, Ch. Deberiotstraat 32, 3000 Leuven, Belgium.

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May 2009

Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

Biol Direct 2008 Oct 8;3:41. Epub 2008 Oct 8.

Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.

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October 2008

Origins and evolution of the formin multigene family that is involved in the formation of actin filaments.

Mol Biol Evol 2008 Dec 6;25(12):2717-33. Epub 2008 Oct 6.

Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, USA.

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December 2008

U12 intron positions are more strongly conserved between animals and plants than U2 intron positions.

Biol Direct 2008 May 14;3:19. Epub 2008 May 14.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

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May 2008

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.

Authors:
Chisato Yamasaki Katsuhiko Murakami Yasuyuki Fujii Yoshiharu Sato Erimi Harada Jun-ichi Takeda Takayuki Taniya Ryuichi Sakate Shingo Kikugawa Makoto Shimada Motohiko Tanino Kanako O Koyanagi Roberto A Barrero Craig Gough Hong-Woo Chun Takuya Habara Hideki Hanaoka Yosuke Hayakawa Phillip B Hilton Yayoi Kaneko Masako Kanno Yoshihiro Kawahara Toshiyuki Kawamura Akihiro Matsuya Naoki Nagata Kensaku Nishikata Akiko Ogura Noda Shin Nurimoto Naomi Saichi Hiroaki Sakai Ryoko Sanbonmatsu Rie Shiba Mami Suzuki Kazuhiko Takabayashi Aiko Takahashi Takuro Tamura Masayuki Tanaka Susumu Tanaka Fusano Todokoro Kaori Yamaguchi Naoyuki Yamamoto Toshihisa Okido Jun Mashima Aki Hashizume Lihua Jin Kyung-Bum Lee Yi-Chueh Lin Asami Nozaki Katsunaga Sakai Masahito Tada Satoru Miyazaki Takashi Makino Hajime Ohyanagi Naoki Osato Nobuhiko Tanaka Yoshiyuki Suzuki Kazuho Ikeo Naruya Saitou Hideaki Sugawara Claire O'Donovan Tamara Kulikova Eleanor Whitfield Brian Halligan Mary Shimoyama Simon Twigger Kei Yura Kouichi Kimura Tomohiro Yasuda Tetsuo Nishikawa Yutaka Akiyama Chie Motono Yuri Mukai Hideki Nagasaki Makiko Suwa Paul Horton Reiko Kikuno Osamu Ohara Doron Lancet Eric Eveno Esther Graudens Sandrine Imbeaud Marie Anne Debily Yoshihide Hayashizaki Clara Amid Michael Han Andreas Osanger Toshinori Endo Michael A Thomas Mika Hirakawa Wojciech Makalowski Mitsuteru Nakao Nam-Soon Kim Hyang-Sook Yoo Sandro J De Souza Maria de Fatima Bonaldo Yoshihito Niimura Vladimir Kuryshev Ingo Schupp Stefan Wiemann Matthew Bellgard Masafumi Shionyu Libin Jia Danielle Thierry-Mieg Jean Thierry-Mieg Lukas Wagner Qinghua Zhang Mitiko Go Shinsei Minoshima Masafumi Ohtsubo Kousuke Hanada Peter Tonellato Takao Isogai Ji Zhang Boris Lenhard Sangsoo Kim Zhu Chen Ursula Hinz Anne Estreicher Kenta Nakai Izabela Makalowska Winston Hide Nicola Tiffin Laurens Wilming Ranajit Chakraborty Marcelo Bento Soares Maria Luisa Chiusano Yutaka Suzuki Charles Auffray Yumi Yamaguchi-Kabata Takeshi Itoh Teruyoshi Hishiki Satoshi Fukuchi Ken Nishikawa Sumio Sugano Nobuo Nomura Yoshio Tateno Tadashi Imanishi Takashi Gojobori

Nucleic Acids Res 2008 Jan 18;36(Database issue):D793-9. Epub 2007 Dec 18.

Japan Biological Information Research Center, Japan Biological Informatics Consortium, Japan.

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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

Functional persistence of exonized mammalian-wide interspersed repeat elements (MIRs).

Genome Res 2007 Aug 10;17(8):1139-45. Epub 2007 Jul 10.

Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany.

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August 2007

What is "junk" DNA, and what is it worth?

Sci Am 2007 May;296(5):104

Pennsylvania State University, USA.

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May 2007

Spliceosomal small nuclear RNA genes in 11 insect genomes.

RNA 2007 Jan 9;13(1):5-14. Epub 2006 Nov 9.

Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742-5815, USA.

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January 2007

Do transposable elements really contribute to proteomes?

Trends Genet 2006 May 29;22(5):260-7. Epub 2006 Mar 29.

Institute of Molecular Evolutionary Genetics and Department of Biology, Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.

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May 2006

Transposable elements as a significant source of transcription regulating signals.

Gene 2006 Jan 10;365:104-10. Epub 2006 Jan 10.

Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.

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January 2006

Origin and evolution of the chicken leukocyte receptor complex.

Proc Natl Acad Sci U S A 2005 Mar 7;102(11):4057-62. Epub 2005 Mar 7.

Institute of Molecular Evolutionary Genetics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.

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March 2005

Eighty percent of proteins are different between humans and chimpanzees.

Gene 2005 Feb;346:215-9

Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802, USA.

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February 2005

Overlapping genes in vertebrate genomes.

Comput Biol Chem 2005 Feb;29(1):1-12

The Huck Institute of the Life Sciences, The Pennsylvania State University, 502 Wartik Lab, University Park, PA 16802, USA.

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February 2005

Does the AD7c-NTP locus encode a protein?

Biochim Biophys Acta 2005 Jan 31;1727(1):1-4. Epub 2004 Dec 31.

Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56, Münster, Germany.

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January 2005

DED: Database of Evolutionary Distances.

Nucleic Acids Res 2005 Jan;33(Database issue):D442-6

Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.

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January 2005

Visualizing sequence similarity of protein families.

Genome Res 2004 Jun 12;14(6):1160-9. Epub 2004 May 12.

Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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June 2004

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

Authors:
Tadashi Imanishi Takeshi Itoh Yutaka Suzuki Claire O'Donovan Satoshi Fukuchi Kanako O Koyanagi Roberto A Barrero Takuro Tamura Yumi Yamaguchi-Kabata Motohiko Tanino Kei Yura Satoru Miyazaki Kazuho Ikeo Keiichi Homma Arek Kasprzyk Tetsuo Nishikawa Mika Hirakawa Jean Thierry-Mieg Danielle Thierry-Mieg Jennifer Ashurst Libin Jia Mitsuteru Nakao Michael A Thomas Nicola Mulder Youla Karavidopoulou Lihua Jin Sangsoo Kim Tomohiro Yasuda Boris Lenhard Eric Eveno Yoshiyuki Suzuki Chisato Yamasaki Jun-ichi Takeda Craig Gough Phillip Hilton Yasuyuki Fujii Hiroaki Sakai Susumu Tanaka Clara Amid Matthew Bellgard Maria de Fatima Bonaldo Hidemasa Bono Susan K Bromberg Anthony J Brookes Elspeth Bruford Piero Carninci Claude Chelala Christine Couillault Sandro J de Souza Marie-Anne Debily Marie-Dominique Devignes Inna Dubchak Toshinori Endo Anne Estreicher Eduardo Eyras Kaoru Fukami-Kobayashi Gopal R Gopinath Esther Graudens Yoonsoo Hahn Michael Han Ze-Guang Han Kousuke Hanada Hideki Hanaoka Erimi Harada Katsuyuki Hashimoto Ursula Hinz Momoki Hirai Teruyoshi Hishiki Ian Hopkinson Sandrine Imbeaud Hidetoshi Inoko Alexander Kanapin Yayoi Kaneko Takeya Kasukawa Janet Kelso Paul Kersey Reiko Kikuno Kouichi Kimura Bernhard Korn Vladimir Kuryshev Izabela Makalowska Takashi Makino Shuhei Mano Regine Mariage-Samson Jun Mashima Hideo Matsuda Hans-Werner Mewes Shinsei Minoshima Keiichi Nagai Hideki Nagasaki Naoki Nagata Rajni Nigam Osamu Ogasawara Osamu Ohara Masafumi Ohtsubo Norihiro Okada Toshihisa Okido Satoshi Oota Motonori Ota Toshio Ota Tetsuji Otsuki Dominique Piatier-Tonneau Annemarie Poustka Shuang-Xi Ren Naruya Saitou Katsunaga Sakai Shigetaka Sakamoto Ryuichi Sakate Ingo Schupp Florence Servant Stephen Sherry Rie Shiba Nobuyoshi Shimizu Mary Shimoyama Andrew J Simpson Bento Soares Charles Steward Makiko Suwa Mami Suzuki Aiko Takahashi Gen Tamiya Hiroshi Tanaka Todd Taylor Joseph D Terwilliger Per Unneberg Vamsi Veeramachaneni Shinya Watanabe Laurens Wilming Norikazu Yasuda Hyang-Sook Yoo Marvin Stodolsky Wojciech Makalowski Mitiko Go Kenta Nakai Toshihisa Takagi Minoru Kanehisa Yoshiyuki Sakaki John Quackenbush Yasushi Okazaki Yoshihide Hayashizaki Winston Hide Ranajit Chakraborty Ken Nishikawa Hideaki Sugawara Yoshio Tateno Zhu Chen Michio Oishi Peter Tonellato Rolf Apweiler Kousaku Okubo Lukas Wagner Stefan Wiemann Robert L Strausberg Takao Isogai Charles Auffray Nobuo Nomura Takashi Gojobori Sumio Sugano

PLoS Biol 2004 Jun 20;2(6):e162. Epub 2004 Apr 20.

Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.

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June 2004

Mammalian overlapping genes: the comparative perspective.

Genome Res 2004 Feb;14(2):280-6

Institute of Molecular Evolutionary Genetics, Department of Biology, Pennsylvania State University, State College, University Park, Pennsylvania 16802, USA.

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February 2004

Mastering seeds for genomic size nucleotide BLAST searches.

Nucleic Acids Res 2003 Dec;31(23):6935-41

Institute of Molecular Evolutionary Genetics and Department of Biology, The Pennsylvania State University, 514 Mueller Lab, University Park, PA 16802, USA.

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December 2003

Transposable elements and vertebrate protein diversity.

Genetica 2003 Jul;118(2-3):183-91

Department of Biology and Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802, USA.

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July 2003

Genomics. Not junk after all.

Science 2003 May;300(5623):1246-7

Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, PA 16802, USA.

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May 2003

Molecular archeology of L1 insertions in the human genome.

Genome Biol 2002 Sep 19;3(10):research0052. Epub 2002 Sep 19.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

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September 2002