Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations

Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila

(2019) Gabriel E. Rech et al.   PLoS Genetics

Genome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication

(2019) Diane A. Flasch et al.   CELL

Recent secondary contacts, linked selection and variable recombination rates shape genomic diversity in the model species Anolis carolinensis

(2019) Yann Bourgeois et al.   Genome Biology and Evolution

The Landscape of L1 Retrotransposons in the Human Genome Is Shaped by Pre-insertion Sequence Biases and Post-insertion Selection

(2019) Tania Sultana et al.   MOLECULAR CELL

Selection at behavioural, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer

(2019) Yann Bourgeois et al.   MOLECULAR ECOLOGY

On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements

(2019) Yann Bourgeois et al.   Genes

Evolutionary Conflict between Mobile DNA and Host Genomes

(2018) Michael J. Song et al.   AMERICAN NATURALIST

Comparative Genomics Reveals Accelerated Evolution in Conserved Pathways during the Diversification of Anole Lizards

(2018) Marc Tollis et al.   Genome Biology and Evolution

Differential Effect of Selection against LINE Retrotransposons among Vertebrates Inferred from Whole-Genome Data and Demographic Modeling

(2018) Alexander T Xue et al.   Genome Biology and Evolution

Multiple and Independent Phases of Transposable Element Amplification in the Genomes of Piciformes (Woodpeckers and Allies)

(2018) Joseph D Manthey et al.   Genome Biology and Evolution

Detecting Signatures of Positive Selection along Defined Branches of a Population Tree Using LSD

(2018) Pablo Librado et al.   MOLECULAR BIOLOGY AND EVOLUTION

Neutral Theory, Transposable Elements, and Eukaryotic Genome Evolution

(2018) Irina R Arkhipova   MOLECULAR BIOLOGY AND EVOLUTION

Supervised Machine Learning for Population Genetics: A New Paradigm

(2018) Daniel R. Schrider et al.   TRENDS IN GENETICS

SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model

(2018) Benjamin C Haller et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution and Diversity of Transposable Elements in Vertebrate Genomes

(2017) Cibele G. Sotero-Caio et al.   Genome Biology and Evolution

Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes

(2017) Alexander Suh et al.   MOLECULAR ECOLOGY

Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds

(2017) Takeshi Kawakami et al.   MOLECULAR ECOLOGY

Transposable Element Domestication As an Adaptation to Evolutionary Conflicts

(2017) Diwash Jangam et al.   TRENDS IN GENETICS

Chromatin states shape insertion profiles of the piggyBac, Tol2 and Sleeping Beauty transposons and murine leukemia virus

(2017) Junko Yoshida et al.   Scientific Reports

LINE Insertion Polymorphisms are Abundant but at Low Frequencies across Populations of Anolis carolinensis

(2017) Robert P. Ruggiero et al.   Frontiers in Genetics

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions

(2016) Sean Hoban et al.   AMERICAN NATURALIST

De novo nonsense and frameshift variants of TCF20 in individuals with intellectual disability and postnatal overgrowth

(2016) Johanna Schäfgen et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

The Evolution of Line-1 in Vertebrates

(2016) Stéphane Boissinot et al.   Genome Biology and Evolution

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

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

Diversification in wild populations of the model organism Anolis carolinensis : A genome-wide phylogeographic investigation

(2016) Joseph D. Manthey et al.   Ecology and Evolution

Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates

(2015) M. Gautier   GENETICS

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum ofFicedulaflycatchers

(2015) Reto Burri et al.   GENOME RESEARCH

Population Genomics of Transposable Elements inDrosophila

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

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

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

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

(2014) Tami E. Cruickshank et al.   MOLECULAR ECOLOGY

Genetic variation in the green anole lizard (Anolis carolinensis) reveals island refugia and a fragmented Florida during the quaternary

(2013) Marc Tollis et al.   GENETICA

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

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

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

(2012) Robert Kofler et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

The genome of the green anole lizard and a comparative analysis with birds and mammals

(2011) Jessica Alföldi et al.   NATURE

Access to DNA establishes a secondary target site bias for the yeast retrotransposon Ty5

(2011) J. A. Baller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Are Transposable Element Insertions Homoplasy Free?: An Examination Using the Avian Tree of Life

(2011) Kin-Lan Han et al.   SYSTEMATIC BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Population Genomics of Transposable Elements in Drosophila melanogaster

(2010) D. A. Petrov et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2010) Josefa González et al.   PLoS Genetics

The adaptive role of transposable elements in the Drosophila genome

(2009) Josefa González et al.   GENE

Regulator of differentiation 1 (ROD1) binds to the amphipathic C-terminal peptide of thrombospondin-4 and is involved in its mitogenic activity

(2009) Gulzhakhan Sadvakassova et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Dynamics of transposable elements: towards a community ecology of the genome

(2009) Samuel Venner et al.   TRENDS IN GENETICS

Distribution of the transposable elements bilbo and gypsy in original and colonizing populations of Drosophila subobscura

(2008) María Pilar García Guerreiro et al.   BMC EVOLUTIONARY BIOLOGY

Contrasting Patterns of Transposable-Element Insertion Polymorphism and Nucleotide Diversity in Autotetraploid and Allotetraploid Arabidopsis Species

(2008) K. M. Hazzouri et al.   GENETICS

The Effects of Recombination Rate on the Distribution and Abundance of Transposable Elements

(2008) E. S. Dolgin et al.   GENETICS

A common sequence motif associated with recombination hot spots and genome instability in humans

(2008) Simon Myers et al.   NATURE 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

High Rate of Recent Transposable Element–Induced Adaptation in Drosophila melanogaster

(2008) Josefa González et al.   PLOS BIOLOGY