Publications by authors named "Alfredo Ruiz"

38Publications

Computational Sequence Analysis of Inversion Breakpoint Regions in the Cactophilic Drosophila mojavensis Lineage.

J Hered 2019 01;110(1):102-117

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.

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January 2019

Genome-Wide Patterns of Sequence Divergence of Protein-Coding Genes Between Drosophila buzzatii and D. mojavensis.

J Hered 2019 01;110(1):92-101

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.

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January 2019

Concurrent Duplication of Drosophila Cid and Cenp-C Genes Resulted in Accelerated Evolution and Male Germline-Biased Expression of the New Copies.

J Mol Evol 2018 07 23;86(6):353-364. Epub 2018 Jun 23.

Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.

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July 2018

Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes.

BMC Genomics 2016 05 10;17:344. Epub 2016 May 10.

Department de Genética i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.

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May 2016

Reassignment of Drosophila willistoni Genome Scaffolds to Chromosome II Arms.

G3 (Bethesda) 2015 Oct 4;5(12):2559-66. Epub 2015 Oct 4.

Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Brazil 15053

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October 2015

Structural and sequence diversity of the transposon Galileo in the Drosophila willistoni genome.

BMC Genomics 2014 Sep 13;15:792. Epub 2014 Sep 13.

Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), CP 15053, Porto Alegre, Rio Grande do Sul 91501-970, Brazil.

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September 2014

Tetris is a foldback transposon that provided the building blocks for an emerging satellite DNA of Drosophila virilis.

Genome Biol Evol 2014 May 24;6(6):1302-13. Epub 2014 May 24.

Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil

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May 2014

BuT2 is a member of the third major group of hAT transposons and is involved in horizontal transfer events in the genus Drosophila.

Genome Biol Evol 2014 Feb;6(2):352-65

Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.

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February 2014

A divergent P element and its associated MITE, BuT5, generate chromosomal inversions and are widespread within the Drosophila repleta species group.

Genome Biol Evol 2013 ;5(6):1127-41

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.

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December 2013

Identification of multiple binding sites for the THAP domain of the Galileo transposase in the long terminal inverted-repeats.

Gene 2013 Aug 4;525(1):84-91. Epub 2013 May 4.

School of Biomedical Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK.

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August 2013

Striking structural dynamism and nucleotide sequence variation of the transposon Galileo in the genome of Drosophila mojavensis.

Mob DNA 2013 Feb 4;4(1). Epub 2013 Feb 4.

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Catalunya, 08193, Spain.

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February 2013

Segmental duplication, microinversion, and gene loss associated with a complex inversion breakpoint region in Drosophila.

Mol Biol Evol 2012 Jul 10;29(7):1875-89. Epub 2012 Feb 10.

Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.

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July 2012

Gene alterations at Drosophila inversion breakpoints provide prima facie evidence for natural selection as an explanation for rapid chromosomal evolution.

BMC Genomics 2012 Feb 1;13:53. Epub 2012 Feb 1.

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.

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February 2012

Testing chromosomal phylogenies and inversion breakpoint reuse in Drosophila. The martensis cluster revisited.

Chromosome Res 2011 Feb 11;19(2):251-65. Epub 2011 Mar 11.

Departament de Genètica i de Microbiologia, Facultat de Biociències, Edifici C, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.

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February 2011

The transposon Galileo generates natural chromosomal inversions in Drosophila by ectopic recombination.

PLoS One 2009 Nov 18;4(11):e7883. Epub 2009 Nov 18.

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.

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November 2009

Cloning and sequencing of the breakpoint regions of inversion 5g fixed in Drosophila buzzatii.

Chromosoma 2009 Jun 7;118(3):349-60. Epub 2009 Feb 7.

Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.

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June 2009

The Foldback-like element Galileo belongs to the P superfamily of DNA transposons and is widespread within the Drosophila genus.

Proc Natl Acad Sci U S A 2008 Feb 19;105(8):2957-62. Epub 2008 Feb 19.

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain.

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February 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

Protein polymorphism is negatively correlated with conservation of intronic sequences and complexity of expression patterns in Drosophila melanogaster.

J Mol Evol 2007 May 24;64(5):511-8. Epub 2007 Apr 24.

Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.

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May 2007

HOM-C evolution in Drosophila: is there a need for Hox gene clustering?

Trends Genet 2007 Feb 26;23(2):55-9. Epub 2006 Dec 26.

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.

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February 2007

Fast sequence evolution of Hox and Hox-derived genes in the genus Drosophila.

BMC Evol Biol 2006 Dec 12;6:106. Epub 2006 Dec 12.

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.

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December 2006

Testing chromosomal phylogenies and inversion breakpoint reuse in Drosophila.

Genetics 2007 Jan 8;175(1):167-77. Epub 2006 Oct 8.

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.

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January 2007

Abundance and chromosomal distribution of six Drosophila buzzatii transposons: BuT1, BuT2, BuT3, BuT4, BuT5, and BuT6.

Chromosoma 2006 Oct 14;115(5):403-12. Epub 2006 Jun 14.

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.

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October 2006

Molecular characterization and chromosomal distribution of Galileo, Kepler and Newton, three foldback transposable elements of the Drosophila buzzatii species complex.

Genetics 2005 Apr 3;169(4):2047-59. Epub 2005 Feb 3.

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.

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April 2005

Duplicative and conservative transpositions of larval serum protein 1 genes in the genus Drosophila.

Genetics 2004 Sep;168(1):253-64

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.

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September 2004

[Spotted fever Rickettsiae. Their immunodominant proteins and immune response].

Rev Med Chil 2004 Mar;132(3):381-7

Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán, Av. Itzaes No 490 x 59, CP 97000, Mérida Yucatán, México.

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March 2004

Silencing of a gene adjacent to the breakpoint of a widespread Drosophila inversion by a transposon-induced antisense RNA.

Proc Natl Acad Sci U S A 2004 Jun 7;101(24):9013-8. Epub 2004 Jun 7.

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.

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June 2004

A new split of the Hox gene complex in Drosophila: relocation and evolution of the gene labial.

Mol Biol Evol 2003 Dec 29;20(12):2042-54. Epub 2003 Aug 29.

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) Spain.

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December 2003

Low occurrence of gene transposition events during the evolution of the genus Drosophila.

Evolution 2003 Jun;57(6):1325-35

Department de Genètica i de Microbiologia, Facultat de Ciències, Edifici C, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.

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June 2003

The foldback-like transposon Galileo is involved in the generation of two different natural chromosomal inversions of Drosophila buzzatii.

Mol Biol Evol 2003 May 2;20(5):674-85. Epub 2003 Apr 2.

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.

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May 2003

Chromosomal elements evolve at different rates in the Drosophila genome.

Genetics 2002 Jul;161(3):1137-54

Departament de Genètica i de Microbiologia, Facultat de Ciències-Edifici C, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.

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July 2002

ANTAGONISTIC PLEIOTROPIC EFFECT OF SECOND-CHROMOSOME INVERSIONS ON BODY SIZE AND EARLY LIFE-HISTORY TRAITS IN DROSOPHILA BUZZATII.

Evolution 1998 Feb;52(1):144-154

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.

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February 1998

INVERSION LENGTH AND BREAKPOINT DISTRIBUTION IN THE DROSOPHILA BUZZATII SPECIES COMPLEX: IS INVERSION LENGTH A SELECTED TRAIT?

Evolution 1997 Aug;51(4):1149-1155

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.

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August 1997

MATING PATTERN AND FITNESS-COMPONENT ANALYSIS ASSOCIATED WITH INVERSION POLYMORPHISM IN A NATURAL POPULATION OF DROSOPHILA BUZZATII.

Evolution 1994 Jun;48(3):767-780

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193, Bellaterra (Barcelona), Spain.

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June 1994

REPRODUCTIVE RELATIONSHIPS AMONG TEN SPECIES OF THE DROSOPHILA REPLETA GROUP FROM SOUTH AMERICA AND THE WEST INDIES.

Evolution 1993 Oct;47(5):1616-1624

Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 8193, Bellaterra (Barcelona), Spain.

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October 1993