RepetDB: a unified resource for transposable element references

[1]  D. Schwartz,et al.  Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters , 2017, BMC Genomics.

[2]  F. Arnaud,et al.  From core referencing to data re-use: two French national initiatives to reinforce paleodata stewardship (National Cyber Core Repository and LTER France Retro-Observatory) , 2017 .

[3]  J. McPherson,et al.  Coming of age: ten years of next-generation sequencing technologies , 2016, Nature Reviews Genetics.

[4]  Suzanna E Lewis,et al.  JBrowse: a dynamic web platform for genome visualization and analysis , 2016, Genome Biology.

[5]  Erik Schultes,et al.  The FAIR Guiding Principles for scientific data management and stewardship , 2016, Scientific Data.

[6]  Anil S. Thanki,et al.  transPLANT Resources for Triticeae Genomic Data , 2016, The plant genome.

[7]  Robert D. Finn,et al.  The Dfam database of repetitive DNA families , 2015, Nucleic Acids Res..

[8]  O. Kohany,et al.  Repbase Update, a database of repetitive elements in eukaryotic genomes , 2015, Mobile DNA.

[9]  H. Quesneville,et al.  Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes , 2015, BMC Genomics.

[10]  C. Thermes,et al.  Ten years of next-generation sequencing technology. , 2014, Trends in genetics : TIG.

[11]  H. Quesneville,et al.  PASTEC: An Automatic Transposable Element Classification Tool , 2014, PloS one.

[12]  Sergio Contrino,et al.  InterMine: extensive web services for modern biology , 2014, Nucleic Acids Res..

[13]  Yu Zhang,et al.  P-MITE: a database for plant miniature inverted-repeat transposable elements , 2013, Nucleic Acids Res..

[14]  H. Quesneville,et al.  The wheat powdery mildew genome shows the unique evolution of an obligate biotroph , 2013, Nature Genetics.

[15]  Hadi Quesneville,et al.  GnpIS: an information system to integrate genetic and genomic data from plants and fungi , 2013, Database J. Biol. Databases Curation.

[16]  Nikita S. Vassetzky,et al.  SINEBase: a database and tool for SINE analysis , 2012, Nucleic Acids Res..

[17]  Thomas Nussbaumer,et al.  MIPS PlantsDB: a database framework for comparative plant genome research , 2012, Nucleic Acids Res..

[18]  Sergio Contrino,et al.  InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data , 2012, Bioinform..

[19]  Damon Lisch,et al.  How important are transposons for plant evolution? , 2012, Nature Reviews Genetics.

[20]  M. Platzer,et al.  A major invasion of transposable elements accounts for the large size of the Blumeria graminis f.sp. tritici genome , 2011, Functional & Integrative Genomics.

[21]  B. Gaut,et al.  Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxurians , 2011, Genome biology and evolution.

[22]  T. Flutre,et al.  Considering Transposable Element Diversification in De Novo Annotation Approaches , 2011, PloS one.

[23]  José M. Sempere,et al.  The Gypsy Database (GyDB) of mobile genetic elements: release 2.0 , 2010, Nucleic Acids Res..

[24]  Hikmet Budak,et al.  Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces[W] , 2010, Plant Cell.

[25]  Ahsan Huda,et al.  Analysis of transposable element sequences using CENSOR and RepeatMasker. , 2009, Methods in molecular biology.

[26]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[27]  J. Bennetzen,et al.  A unified classification system for eukaryotic transposable elements , 2007, Nature Reviews Genetics.

[28]  David C. Nickle,et al.  ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets , 2007, Bioinform..

[29]  Zhao Xu,et al.  LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons , 2007, Nucleic Acids Res..

[30]  R. Martienssen,et al.  Transposable elements and the epigenetic regulation of the genome , 2007, Nature Reviews Genetics.

[31]  J. Jurka,et al.  Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.

[32]  Casey M. Bergman,et al.  Combined Evidence Annotation of Transposable Elements in Genome Sequences , 2005, PLoS Comput. Biol..

[33]  Eugene W. Myers,et al.  PILER: identification and classification of genomic repeats , 2005, ISMB.

[34]  P. Bennett.  Genome plasticity: insertion sequence elements, transposons and integrons, and DNA rearrangement. , 2004, Methods in molecular biology.

[35]  C. Robin Buell,et al.  The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants , 2004, Nucleic Acids Res..

[36]  H. Quesneville,et al.  Detection of New Transposable Element Families in Drosophila melanogaster and Anopheles gambiae Genomes , 2003, Journal of Molecular Evolution.

[37]  S. Eddy,et al.  Automated de novo identification of repeat sequence families in sequenced genomes. , 2002, Genome research.

[38]  X. Huang,et al.  On global sequence alignment , 1994, Comput. Appl. Biosci..