Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

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

(2019) Pavel Neumann et al.   Mobile DNA

Redistribution of CHH Methylation and Small Interfering RNAs across the Genome of Tomato ddm1 Mutants

(2018) Shira Corem et al.   PLANT CELL

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution

(2018) Daniel Lang et al.   PLANT JOURNAL

Integration site selection by retroviruses and transposable elements in eukaryotes

(2017) Tania Sultana et al.   NATURE REVIEWS GENETICS

Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin

(2017) Zaida Vergara et al.   NUCLEIC ACIDS RESEARCH

The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization

(2017) Ryan F. McCormick et al.   PLANT JOURNAL

The First Rule of Plant Transposable Element Silencing: Location, Location, Location

(2016) Meredith J. Sigman et al.   PLANT CELL

DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity

(2015) Monica Naughtin et al.   PLoS One

Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data

(2015) Vimal Rawat et al.   PLoS One

An improved genome release (version Mt4.0) for the model legume Medicago truncatula

(2014) Haibao Tang et al.   BMC GENOMICS

Hi-C Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila

(2014) Stefan Grob et al.   MOLECULAR CELL

Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana

(2014) Florian Maumus et al.   Nature Communications

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

Construction of Reference Chromosome-Scale Pseudomolecules for Potato: Integrating the Potato Genome with Genetic and Physical Maps

(2013) Sanjeev Kumar Sharma et al.   G3-Genes Genomes Genetics

Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots

(2012) L. Mularoni et al.   GENOME RESEARCH

A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon

(2012) J. A. Baller et al.   GENOME RESEARCH

Characterization and functional annotation of nested transposable elements in eukaryotic genomes

(2012) Caihua Gao et al.   GENOMICS

Nucleosome Positioning: Multiple Mechanisms toward a Unifying Goal

(2012) Arnob Dutta et al.   MOLECULAR CELL

New Insights into Nested Long Terminal Repeat Retrotransposons in Brassica Species

(2012) Lijuan Wei et al.   Molecular Plant

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

(2012) Andrew H. Paterson et al.   NATURE

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons

(2012) Steven R. Eichten et al.   PLoS Genetics

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

BraSto, a Stowaway MITE from Brassica: recently active copies preferentially accumulate in the gene space

(2011) Véronique Sarilar et al.   PLANT MOLECULAR BIOLOGY

Plant centromeric retrotransposons: a structural and cytogenetic perspective

(2011) Pavel Neumann et al.   Mobile DNA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

(2010) C. Llorens et al.   NUCLEIC ACIDS RESEARCH

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees

(2009) Carlos Llorens et al.   Biology Direct

Target site selection by the mariner-like element, Mos1

(2009) Gwénaelle Crénès et al.   GENETICA

Bursts of retrotransposition reproduced in Arabidopsis

(2009) Sayuri Tsukahara et al.   NATURE

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements

(2009) Asaf Levy et al.   NUCLEIC ACIDS RESEARCH

Contrasting evolutionary dynamics between angiosperm and mammalian genomes

(2009) Eduard Kejnovsky et al.   TRENDS IN ECOLOGY & EVOLUTION

Genome Structure of the Legume, Lotus japonicus

(2008) S. Sato et al.   DNA RESEARCH

Dynamics and Differential Proliferation of Transposable Elements During the Evolution of the B and A Genomes of Wheat

(2008) M. Charles et al.   GENETICS

Chromodomains direct integration of retrotransposons to heterochromatin

(2008) X. Gao et al.   GENOME RESEARCH

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

(2008) T. N. Mavrich et al.   GENOME RESEARCH

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

(2008) Raquel S. Linheiro et al.   NUCLEIC ACIDS RESEARCH