Publications by authors named "Casey M Bergman"

60Publications

Evolution of Ty1 copy number control in yeast by horizontal transfer and recombination.

PLoS Genet 2020 02 21;16(2):e1008632. Epub 2020 Feb 21.

Institute of Bioinformatics and Department of Genetics, University of Georgia, Athens, Georgia, United States of America.

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February 2020

Complete Genome Assemblies for Three Variants of the Endosymbiont of Drosophila melanogaster.

Microbiol Resour Announc 2019 Nov 7;8(45). Epub 2019 Nov 7.

Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA.

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November 2019

Phased Diploid Genome Assemblies for Three Strains of from Oak Trees.

G3 (Bethesda) 2019 11 5;9(11):3547-3554. Epub 2019 Nov 5.

Department of Plant Biology and Institute of Bioinformatics, University of Georgia, Athens, GA, and

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November 2019

Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion.

Genome Biol 2019 06 21;20(1):127. Epub 2019 Jun 21.

GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France.

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June 2019

Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation.

PLoS Pathog 2018 11 13;14(11):e1007445. Epub 2018 Nov 13.

Department of Cell Biology, Howard Hughes Medical Institute and Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY, United States of America.

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November 2018

Horizontal transfer and proliferation of Tsu4 in Saccharomyces paradoxus.

Authors:
Casey M Bergman

Mob DNA 2018 12;9:18. Epub 2018 Jun 12.

Department of Genetics and Institute of Bioinformatics, University of Georgia, East Green St., Athens, GA, 30602 USA.

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June 2018

Conserved Noncoding Elements Influence the Transposable Element Landscape in Drosophila.

Genome Biol Evol 2018 06;10(6):1533-1545

Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

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June 2018

Genomic analysis of elements in natural populations of .

PeerJ 2017 15;5:e3824. Epub 2017 Sep 15.

Department of General and Molecular Genetics, Taras Shevchenko University of Kyiv, Kyiv, Ukraine.

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September 2017

McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data.

G3 (Bethesda) 2017 08 7;7(8):2763-2778. Epub 2017 Aug 7.

Faculty of Life Sciences, University of Manchester, M13 9PL, United Kingdom

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August 2017

Bringing PLOS Genetics Editors to Preprint Servers.

PLoS Genet 2016 12 1;12(12):e1006448. Epub 2016 Dec 1.

Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, United States of America.

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December 2016

Rare recombination events generate sequence diversity among balancer chromosomes in Drosophila melanogaster.

Proc Natl Acad Sci U S A 2016 Mar 22;113(10):E1352-61. Epub 2016 Feb 22.

Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom

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March 2016

Unique transposon landscapes are pervasive across Drosophila melanogaster genomes.

Nucleic Acids Res 2015 Dec 17;43(22):10655-72. Epub 2015 Nov 17.

Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA

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December 2015

Dynamics of Wolbachia pipientis Gene Expression Across the Drosophila melanogaster Life Cycle.

G3 (Bethesda) 2015 Oct 23;5(12):2843-56. Epub 2015 Oct 23.

Faculty of Life Sciences, University of Manchester, M13 9PT Manchester, United Kingdom

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October 2015

Drosophila innate immunity: regional and functional specialization of prophenoloxidases.

BMC Biol 2015 Oct 1;13:81. Epub 2015 Oct 1.

Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland.

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October 2015

Strain-specific and pooled genome sequences for populations of Drosophila melanogaster from three continents.

F1000Res 2015 29;4:31. Epub 2015 Jan 29.

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK.

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February 2015

An age-of-allele test of neutrality for transposable element insertions.

Genetics 2014 Feb 13;196(2):523-38. Epub 2013 Dec 13.

Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66049.

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February 2014

Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.

PLoS Genet 2012 20;8(12):e1003129. Epub 2012 Dec 20.

Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

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May 2013

Evolutionary genomics of transposable elements in Saccharomyces cerevisiae.

PLoS One 2012 30;7(11):e50978. Epub 2012 Nov 30.

School of Applied Sciences, University of Huddersfield, West Yorkshire, UK.

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May 2013

A proposal for the reference-based annotation of de novo transposable element insertions.

Authors:
Casey M Bergman

Mob Genet Elements 2012 Jan;2(1):51-54

Faculty of Life Sciences; University of Manchester; Manchester, UK.

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January 2012

BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events.

Bioinformatics 2012 Aug 17;28(16):2154-61. Epub 2012 Jun 17.

Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.

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August 2012

Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster.

PLoS One 2012 9;7(2):e30008. Epub 2012 Feb 9.

Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

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July 2012

pubmed2ensembl: a resource for mining the biological literature on genes.

PLoS One 2011 29;6(9):e24716. Epub 2011 Sep 29.

Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

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April 2012

The GNAT library for local and remote gene mention normalization.

Bioinformatics 2011 Oct 3;27(19):2769-71. Epub 2011 Aug 3.

Pharma Research and Early Development, Hoffmann-La Roche Inc., Nutley, NJ 07110, USA.

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October 2011

Annotating genes and genomes with DNA sequences extracted from biomedical articles.

Bioinformatics 2011 Apr 16;27(7):980-6. Epub 2011 Feb 16.

Faculty of Life Sciences, University of Manchester, Manchester, UK.

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April 2011

A large palindrome with interchromosomal gene duplications in the pericentromeric region of the D. melanogaster Y chromosome.

Mol Biol Evol 2011 Jul 5;28(7):1967-71. Epub 2011 Feb 5.

Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.

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July 2011

Gene expression divergence recapitulates the developmental hourglass model.

Nature 2010 Dec;468(7325):811-4

Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.

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December 2010

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila.

Nucleic Acids Res 2011 Jan 21;39(Database issue):D118-23. Epub 2010 Oct 21.

Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York, Buffalo, NY 14203, USA.

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January 2011

Evolutionary systems biology of amino acid biosynthetic cost in yeast.

PLoS One 2010 Aug 17;5(8):e11935. Epub 2010 Aug 17.

Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

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August 2010

The evolution of tRNA genes in Drosophila.

Genome Biol Evol 2010 Jul 12;2:467-77. Epub 2010 Jul 12.

Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

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July 2010

LINNAEUS: a species name identification system for biomedical literature.

BMC Bioinformatics 2010 Feb 11;11:85. Epub 2010 Feb 11.

Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK.

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February 2010

Assigning roles to protein mentions: the case of transcription factors.

J Biomed Inform 2009 Oct 11;42(5):887-94. Epub 2009 Apr 11.

School of Computer Science, University of Manchester, UK.

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October 2009

Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element.

Nucleic Acids Res 2008 Nov 1;36(19):6199-208. Epub 2008 Oct 1.

Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.

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November 2008

Drosophila polymorphism database (DPDB): a portal for nucleotide polymorphism in Drosophila.

Fly (Austin) 2007 Jul-Aug;1(4):205-11. Epub 2007 Jul 17.

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

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November 2008

Text-mining assisted regulatory annotation.

Genome Biol 2008 13;9(2):R31. Epub 2008 Feb 13.

Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven, B-3000, Belgium.

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May 2008

REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila.

Nucleic Acids Res 2008 Jan 26;36(Database issue):D594-8. Epub 2007 Nov 26.

Department of Biochemistry, Department of Biological Sciences, State University of New York at Buffalo, Buffalo NY 14214, 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

Discovering and detecting transposable elements in genome sequences.

Brief Bioinform 2007 Nov 10;8(6):382-92. Epub 2007 Oct 10.

Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.

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November 2007

Purifying selection maintains highly conserved noncoding sequences in Drosophila.

Mol Biol Evol 2007 Oct 23;24(10):2222-34. Epub 2007 Jul 23.

Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester M13 9PT, UK.

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October 2007

Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster.

Proc Natl Acad Sci U S A 2007 Jul 25;104(27):11340-5. Epub 2007 Jun 25.

Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom.

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July 2007

Large-scale discovery of promoter motifs in Drosophila melanogaster.

PLoS Comput Biol 2007 Jan 5;3(1):e7. Epub 2006 Dec 5.

Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.

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January 2007

Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA.

Bioinformatics 2006 Dec 10;22(23):2858-64. Epub 2006 Oct 10.

Institute for Genetics, University of Cologne Zuelpicher Strasse 47, 50674 Cologne, Germany.

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December 2006

Drosophila melanogaster: a case study of a model genomic sequence and its consequences.

Genome Res 2005 Dec;15(12):1661-7

Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom.

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December 2005

Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome.

BMC Biol 2005 Nov 12;3:24. Epub 2005 Nov 12.

Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA.

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November 2005

Combined evidence annotation of transposable elements in genome sequences.

PLoS Comput Biol 2005 Jul 29;1(2):166-75. Epub 2005 Jul 29.

Laboratoire Dynamique du Génome et Evolution, Institut Jacques Monod, Paris, France.

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July 2005

Functional evolution of a cis-regulatory module.

PLoS Biol 2005 Apr 15;3(4):e93. Epub 2005 Mar 15.

Department of Ecology and Evolution, University of Chicago, Illinois, USA.

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April 2005

Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster.

Bioinformatics 2005 Apr 30;21(8):1747-9. Epub 2004 Nov 30.

Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.

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April 2005

Benchmarking tools for the alignment of functional noncoding DNA.

BMC Bioinformatics 2004 01 21;5. Epub 2004 Jan 21.

Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA.

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January 2004

Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites.

Mol Biol Evol 2003 May 2;20(5):703-14. Epub 2003 Apr 2.

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

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May 2003