Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon

On the post-glacial spread of human commensal Arabidopsis thaliana

(2017) Cheng-Ruei Lee et al.   Nature Communications

Genome-wide characterization of non-reference transposons in crops suggests non-random insertion

(2016) Bin Wei et al.   BMC GENOMICS

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

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DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity

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The industrial melanism mutation in British peppered moths is a transposable element

(2016) Arjen E. van’t Hof et al.   NATURE

Robust and scalable inference of population history from hundreds of unphased whole genomes

(2016) Jonathan Terhorst et al.   NATURE GENETICS

Genetic drift, selection and the evolution of the mutation rate

(2016) Michael Lynch et al.   NATURE REVIEWS GENETICS

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

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

Adaptation to Global Change: A Transposable Element–Epigenetics Perspective

(2016) Olivier Rey et al.   TRENDS IN ECOLOGY & EVOLUTION

Multiple Independent Retroelement Insertions in the Promoter of a Stress Response Gene Have Variable Molecular and Functional Effects in Drosophila

(2016) Miriam Merenciano et al.   PLoS Genetics

Brachypodium distachyonandSetaria viridis: Model Genetic Systems for the Grasses

(2015) Thomas P. Brutnell et al.   Annual Review of Plant Biology

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?

(2015) O Mazet et al.   HEREDITY

Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome

(2015) Walter Sanseverino et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of the mating system in colonizing plants

(2015) John R. Pannell   MOLECULAR ECOLOGY

Tempo and Mode of Transposable Element Activity in Drosophila

(2015) Robert Kofler et al.   PLoS Genetics

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

(2015) Irina Makarevitch et al.   PLoS Genetics

Population Genomics of Transposable Elements inDrosophila

(2014) Maite G. Barrón et al.   Annual Review of Genetics

Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach

(2014) Matteo Dell’Acqua et al.   BMC GENOMICS

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data

(2014) Tae-Ho Lee et al.   BMC GENOMICS

The bright side of transposons in crop evolution

(2014) C. Vitte et al.   Briefings in Functional Genomics

Widespread and frequent horizontal transfers of transposable elements in plants

(2014) M. El Baidouri et al.   GENOME RESEARCH

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

TEMP: a computational method for analyzing transposable element polymorphism in populations

(2014) Jiali Zhuang et al.   NUCLEIC ACIDS RESEARCH

Patterns and processes in plant phylogeography in the Mediterranean Basin. A review

(2014) Gonzalo Nieto Feliner   PERSPECTIVES IN PLANT ECOLOGY EVOLUTION AND SYSTEMATICS

Transposable element islands facilitate adaptation to novel environments in an invasive species

(2014) Lukas Schrader et al.   Nature Communications

An Age-of-Allele Test of Neutrality for Transposable Element Insertions

(2013) J. P. Blumenstiel et al.   GENETICS

Comparative Genomic Paleontology across Plant Kingdom Reveals the Dynamics of TE-Driven Genome Evolution

(2013) Moaine El Baidouri et al.   Genome Biology and Evolution

Abundance and Distribution of Transposable Elements in Two Drosophila QTL Mapping Resources

(2013) Julie M. Cridland et al.   MOLECULAR BIOLOGY AND EVOLUTION

The impact of transposable elements in environmental adaptation

(2013) Elena Casacuberta et al.   MOLECULAR ECOLOGY

Transposable elements and microevolutionary changes in natural populations

(2013) Georgi Bonchev et al.   Molecular Ecology Resources

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

Genome-Wide Characterization of Nonreference Transposons Reveals Evolutionary Propensities of Transposons in Soybean

(2012) Z. Tian et al.   PLANT CELL

Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster

(2012) Robert Kofler et al.   PLoS Genetics

Climate Relicts: Past, Present, Future

(2011) Arndt Hampe et al.   Annual Review of Ecology Evolution and Systematics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxurians

(2011) Maud I. Tenaillon et al.   Genome Biology and Evolution

Miniature Inverted-Repeat Transposable Elements (MITEs) Have Been Accumulated through Amplification Bursts and Play Important Roles in Gene Expression and Species Diversity in Oryza sativa

(2011) C. Lu et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans

(2011) Chip Stewart et al.   PLoS Genetics

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

A triptych of the evolution of plant transposable elements

(2010) Maud I. Tenaillon et al.   TRENDS IN PLANT SCIENCE

Genome-Wide Patterns of Adaptation to Temperate Environments Associated with Transposable Elements in Drosophila

(2010) Josefa González et al.   PLoS Genetics

Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon

(2009) John P Vogel et al.   BMC PLANT BIOLOGY

Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression

(2009) J. D. Hollister et al.   GENOME RESEARCH

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Epigenetic Regulation of Transposable Elements in Plants

(2008) Damon Lisch   Annual Review of Plant Biology

Genomic Consequences of Outcrossing and Selfing in Plants

(2008) Stephen I. Wright et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata

(2008) S. Lockton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Retrotransposon-Mediated Gene Duplication Underlies Morphological Variation of Tomato Fruit

(2008) H. Xiao et al.   SCIENCE