Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification

Ortervirales : New Virus Order Unifying Five Families of Reverse-Transcribing Viruses

(2018) Mart Krupovic et al.   JOURNAL OF VIROLOGY

Nomenclature for endogenous retrovirus (ERV) loci

(2018) Robert J. Gifford et al.   Retrovirology

LTR-retrotransposons in plants: Engines of evolution

(2017) Leonardo Galindo-González et al.   GENE

SMS: Smart Model Selection in PhyML

(2017) Vincent Lefort et al.   MOLECULAR BIOLOGY AND EVOLUTION

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

(2016) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Convergent Evolution of Ribonuclease H in LTR Retrotransposons and Retroviruses

(2015) Kirill Ustyantsev et al.   MOLECULAR BIOLOGY AND EVOLUTION

Analysis of the giant genomes ofFritillaria(Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size

(2015) Laura J. Kelly et al.   NEW PHYTOLOGIST

From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

(2014) Brad R Ruhfel et al.   BMC EVOLUTIONARY BIOLOGY

A-to-I editing on tRNAs: Biochemical, biological and evolutionary implications

(2014) Adrian Gabriel Torres et al.   FEBS LETTERS

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

Sirevirus LTR retrotransposons: phylogenetic misconceptions in the plant world

(2013) Alexandros Bousios et al.   Mobile DNA

MASiVEdb: the Sirevirus Plant Retrotransposon Database

(2012) Alexandros Bousios et al.   BMC GENOMICS

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

Structure and Mechanisms of Lysine Methylation Recognition by the Chromodomain in Gene Transcription

(2011) Kyoko L. Yap et al.   BIOCHEMISTRY

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story

(2011) Alexandros Bousios et al.   PLANT JOURNAL

Next Generation Sequencing-Based Analysis of Repetitive DNA in the Model Dioceous Plant Silene latifolia

(2011) Jiří Macas et al.   PLoS One

Determinants of tRNA editing and modification: Avoiding conundrums, affecting function

(2011) Zdeněk Paris et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Plant centromeric retrotransposons: a structural and cytogenetic perspective

(2011) Pavel Neumann et al.   Mobile DNA

Evolutionary genomics revealed interkingdom distribution of Tcn1-like chromodomain-containing Gypsy LTR retrotransposons among fungi and plants

(2010) Olga Novikova et al.   BMC GENOMICS

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees

(2009) Carlos Llorens et al.   Biology Direct

Hypervariable 3′ UTR region of plant LTR-retrotransposons as a source of novel satellite repeats

(2009) Jiří Macas et al.   GENE

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

(2009) Regina S. Baucom et al.   PLoS Genetics

PatMaN: rapid alignment of short sequences to large databases

(2008) Kay Prüfer et al.   BIOINFORMATICS

Structure and dynamics of retrotransposons at wheat centromeres and pericentromeres

(2008) Zhao Liu et al.   CHROMOSOMA

Chromodomains direct integration of retrotransposons to heterochromatin

(2008) X. Gao et al.   GENOME RESEARCH

Experimental evidence for splicing of intron-containing transcripts of plant LTR retrotransposon Ogre

(2008) Veronika Steinbauerová et al.   MOLECULAR GENETICS AND GENOMICS

The diversity of retrotransposons and the properties of their reverse transcriptases

(2008) Thomas H. Eickbush et al.   VIRUS RESEARCH