Transposable Element Annotation in Completely Sequenced Eukaryote Genomes
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Hadi Quesneville | Timothée Flutre | Emmanuelle Permal | T. Flutre | H. Quesneville | E. Permal | Emmanuelle Permal
[1] Anna-Sophie Fiston-Lavier,et al. A model of segmental duplication formation in Drosophila melanogaster. , 2007, Genome research.
[2] Eugene W. Myers,et al. PILER : identification and classification of genomic repeats , 2005 .
[3] J. V. Moran,et al. Initial sequencing and analysis of the human genome. , 2001, Nature.
[4] P. Hooykaas,et al. An Arabidopsis hAT-like transposase is essential for plant development , 2005, Nature.
[5] S. Eddy,et al. Automated de novo identification of repeat sequence families in sequenced genomes. , 2002, Genome research.
[6] X. Huang,et al. On global sequence alignment , 1994, Comput. Appl. Biosci..
[7] J. Bennetzen,et al. A unified classification system for eukaryotic transposable elements , 2007, Nature Reviews Genetics.
[8] Sean R. Eddy,et al. Pack-MULE transposable elements mediate gene evolution in plants , 2004, Nature.
[9] F. Zhou,et al. MUST: a system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi. , 2009, Gene.
[10] E. Lerat. Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs , 2010, Heredity.
[11] Y. Gray,et al. It takes two transposons to tango: transposable-element-mediated chromosomal rearrangements. , 2000, Trends in genetics : TIG.
[12] Haixu Tang,et al. MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes , 2009, Nucleic acids research.
[13] Robert C. Edgar,et al. MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.
[14] A. Hikosaka,et al. A systematic search and classification of T2 family miniature inverted-repeat transposable elements (MITEs) in Xenopus tropicalis suggests the existence of recently active MITE subfamilies , 2009, Molecular Genetics and Genomics.
[15] Zhao Xu,et al. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons , 2007, Nucleic Acids Res..
[16] H. Quesneville,et al. Detection of New Transposable Element Families in Drosophila melanogaster and Anopheles gambiae Genomes , 2003, Journal of Molecular Evolution.
[17] Christina A. Cuomo,et al. Obligate biotrophy features unraveled by the genomic analysis of rust fungi , 2011, Proceedings of the National Academy of Sciences.
[18] S Wright,et al. Transposon diversity in Arabidopsis thaliana. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[19] Graziano Pesole,et al. Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita , 2008, Nature Biotechnology.
[20] Melanie A. Huntley,et al. Evolution of genes and genomes on the Drosophila phylogeny , 2007, Nature.
[21] Eugene W. Myers,et al. Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length , 2005, RECOMB.
[22] Z. Tu,et al. Eight novel families of miniature inverted repeat transposable elements in the African malaria mosquito, Anopheles gambiae. , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[23] W. Lathe,et al. Evolution of R1 and R2 in the rDNA units of the genus Drosophila , 2004, Genetica.
[24] Dawn H. Nagel,et al. The B73 Maize Genome: Complexity, Diversity, and Dynamics , 2009, Science.
[25] Y. Van de Peer,et al. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis , 2008, Nature.
[26] Susan R. Wessler,et al. MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences , 2010, Nucleic acids research.
[27] Kim R. Rasmussen,et al. Efficient q-Gram Filters for Finding All-Matches Over a Given Length , 2005 .
[28] John F. McDonald,et al. LTR_STRUC: a novel search and identification program for LTR retrotransposons , 2003, Bioinform..
[29] Srinivas Aluru,et al. Efficient algorithms and software for detection of full-length LTR retrotransposons , 2006, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05).
[30] Lior Pachter,et al. Identification of transposable elements using multiple alignments of related genomes. , 2005, Genome research.
[31] G. Benson,et al. Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.
[32] J. Jurka,et al. RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons , 2005, PLoS biology.
[33] György Abrusán,et al. TEclass - a tool for automated classification of unknown eukaryotic transposable elements , 2009, Bioinform..
[34] O. Gascuel,et al. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.
[35] Jian Wang,et al. ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun , 2005, PLoS Comput. Biol..
[36] S. Jackson,et al. Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. , 2006, Genome research.
[37] Bernard Henrissat,et al. Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea , 2011, PLoS genetics.
[38] A PevznerPavel,et al. De novo identification of repeat families in large genomes , 2005 .
[39] T. Flutre,et al. Considering Transposable Element Diversification in De Novo Annotation Approaches , 2011, PloS one.
[40] Fred Dyda,et al. Transposition of hAT elements links transposable elements and V(D)J recombination , 2004, Nature.
[41] Gregory Kucherov,et al. mreps: efficient and flexible detection of tandem repeats in DNA , 2003, Nucleic Acids Res..
[42] S. Kurtz,et al. A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes , 2008, BMC Genomics.
[43] International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome , 2001, Nature.
[44] Stefan Kurtz,et al. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons , 2008, BMC Bioinformatics.
[45] Corinne Da Silva,et al. The Ectocarpus genome and the independent evolution of multicellularity in brown algae , 2010, Nature.
[46] D. Petrov. Evolution of genome size: new approaches to an old problem. , 2001, Trends in genetics : TIG.
[47] Guillaume Bourque,et al. Transposable elements in gene regulation and in the evolution of vertebrate genomes. , 2009, Current opinion in genetics & development.
[48] Jonathan Perreault,et al. RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures , 2007, Nucleic Acids Res..
[49] L. Holm,et al. The Pfam protein families database , 2005, Nucleic Acids Res..
[50] D. Finnegan,et al. Eukaryotic transposable elements and genome evolution. , 1989, Trends in genetics : TIG.
[51] V. Pereira. Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome , 2004, Genome Biology.
[52] Wanjun Gu,et al. Identification of repeat structure in large genomes using repeat probability clouds. , 2008, Analytical biochemistry.
[53] Srinivas Aluru,et al. Efficient Algorithms and Software for Detection of Full-Length LTR Retrotransposons , 2005, CSB.
[54] K. Katoh,et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.
[55] Jef D Boeke,et al. Molecular archeology of L1 insertions in the human genome , 2002, Genome Biology.
[56] M. Lynch,et al. De novo identification of LTR retrotransposons in eukaryotic genomes , 2007, BMC Genomics.
[57] Guojun Yang,et al. Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes , 2011, Chromosome Research.
[58] William Lee,et al. Genome-tools: a flexible package for genome sequence analysis. , 2002, BioTechniques.
[59] Guojun Yang,et al. MAK, a computational tool kit for automated MITE analysis , 2003, Nucleic Acids Res..
[60] Chunhong Mao,et al. The Changing Tails of a Novel Short Interspersed Element in Aedes aegypti , 2004, Genetics.
[61] M. Morgante,et al. Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize , 2005, Nature Genetics.
[62] V. Pereira. Automated paleontology of repetitive DNA with REANNOTATE , 2008, BMC Genomics.
[63] Casey M. Bergman,et al. Combined Evidence Annotation of Transposable Elements in Genome Sequences , 2005, PLoS Comput. Biol..
[64] Jason S. Caronna,et al. Computational prediction and molecular confirmation of Helitron transposons in the maize genome , 2008, BMC Genomics.
[65] Jean,et al. Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations , 2011, Nature communications.
[66] Christina A. Cuomo,et al. Obligate Biotrophy Features Unraveled by the Genomic Analysis of the Rust Fungi, Melampsora larici-populina and Puccinia graminis f. sp. tritici , 2011 .
[67] Elena R. Lozovsky,et al. Patterns of insertion and deletion in contrasting chromatin domains. , 2002, Molecular biology and evolution.
[68] Geoffrey J. Barton,et al. The Jalview Java alignment editor , 2004, Bioinform..
[69] Bernard Henrissat,et al. Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis , 2010, Nature.
[70] C. Feschotte. Transposable elements and the evolution of regulatory networks , 2008, Nature Reviews Genetics.
[71] Jerzy Jurka,et al. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor , 2006, BMC Bioinformatics.
[72] J. Jurka,et al. Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.
[73] F. Crick,et al. Selfish DNA: the ultimate parasite , 1980, Nature.
[74] E. Birney,et al. Pfam: the protein families database , 2013, Nucleic Acids Res..
[75] J. Casacuberta,et al. Genome-wide analysis of the Emigrant family of MITEs of Arabidopsis thaliana. , 2002, Molecular biology and evolution.
[76] Nicola Vitacolonna,et al. Structured motifs search , 2004, J. Comput. Biol..
[77] S. Kurtz,et al. Fine-grained annotation and classification of de novo predicted LTR retrotransposons , 2009, Nucleic acids research.
[78] Christina A. Cuomo,et al. The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization , 2007, Science.
[79] M. Low,et al. Ancient Exaptation of a CORE-SINE Retroposon into a Highly Conserved Mammalian Neuronal Enhancer of the Proopiomelanocortin Gene , 2007, PLoS genetics.
[80] Jerzy Jurka,et al. Censor - a Program for Identification and Elimination of Repetitive Elements From DNA Sequences , 1996, Comput. Chem..
[81] J. Bennetzen,et al. Structure-based discovery and description of plant and animal Helitrons , 2009, Proceedings of the National Academy of Sciences.
[82] Pari Skamnioti,et al. Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism , 2010, Science.
[83] Casey M. Bergman,et al. Discovering and detecting transposable elements in genome sequences , 2007, Briefings Bioinform..
[84] Michael Ashburner,et al. Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome , 2006, Genome Biology.
[85] Nirmal Ranganathan,et al. Exploring Repetitive DNA Landscapes Using REPCLASS, a Tool That Automates the Classification of Transposable Elements in Eukaryotic Genomes , 2009, Genome biology and evolution.
[86] Evgeny M. Zdobnov,et al. Genome Sequence of Aedes aegypti, a Major Arbovirus Vector , 2007, Science.