T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data

Tangram: a comprehensive toolbox for mobile element insertion detection

(2014) Jiantao Wu et al.   BMC GENOMICS

The transposable elementBari-Jhehmediates oxidative stress response in Drosophila

(2014) Lain Guio et al.   MOLECULAR ECOLOGY

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

(2014) Jiali Zhuang et al.   NUCLEIC ACIDS RESEARCH

A Transposable Element Insertion Confers Xenobiotic Resistance in Drosophila

(2014) Lidia Mateo et al.   PLoS Genetics

How do mammalian transposons induce genetic variation? A conceptual framework

(2013) Keiko Akagi et al.   BIOESSAYS

The Next-Generation Sequencing Revolution and Its Impact on Genomics

(2013) Daniel C. Koboldt et al.   CELL

The impact of transposable elements in environmental adaptation

(2013) Elena Casacuberta et al.   MOLECULAR ECOLOGY

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

The Use of RelocaTE and Unassembled Short Reads to Produce High-Resolution Snapshots of Transposable Element Generated Diversity in Rice

(2013) Sofia M. C. Robb et al.   G3-Genes Genomes Genetics

Transposable Elements Re-Wire and Fine-Tune the Transcriptome

(2013) Michael Cowley et al.   PLoS Genetics

RetroSeq: transposable element discovery from next-generation sequencing data

(2012) Thomas M. Keane et al.   BIOINFORMATICS

The impact of transposable elements on eukaryotic genomes: From genome size increase to genetic adaptation to stressful environments

(2012) Benoît Chénais et al.   GENE

The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

Whole Genome Resequencing Reveals Natural Target Site Preferences of Transposable Elements in Drosophila melanogaster

(2012) Raquel S. Linheiro et al.   PLoS One

Empirical Validation of Pooled Whole Genome Population Re-Sequencing in Drosophila melanogaster

(2012) Yuan Zhu et al.   PLoS One

Landscape of Somatic Retrotransposition in Human Cancers

(2012) E. Lee et al.   SCIENCE

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

(2012) Robert Kofler et al.   PLoS Genetics

SHRiMP2: Sensitive yet Practical Short Read Mapping

(2011) Matei David et al.   BIOINFORMATICS

The struggle for life of the genome's selfish architects

(2011) Aurélie Hua-Van et al.   Biology Direct

Genome-wide analysis of mobile genetic element insertion sites

(2011) Kamal Rawal et al.   NUCLEIC ACIDS RESEARCH

Successive Increases in the Resistance of Drosophila to Viral Infection through a Transposon Insertion Followed by a Duplication

(2011) Michael M. Magwire et al.   PLoS Genetics

A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans

(2011) Chip Stewart et al.   PLoS Genetics

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

(2010) Fereydoun Hormozdiari et al.   BIOINFORMATICS

Natural Mutagenesis of Human Genomes by Endogenous Retrotransposons

(2010) Rebecca C. Iskow et al.   CELL

A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution

(2010) C. Biemont   GENETICS

Validation of Rearrangement Break Points Identified by Paired-End Sequencing in Natural Populations of Drosophila melanogaster

(2010) Julie M. Cridland et al.   Genome Biology and Evolution

Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans

(2010) A. D. Ewing et al.   GENOME RESEARCH

Population Genomics of Transposable Elements in Drosophila melanogaster

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

T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data

(2010) Anna-Sophie Fiston-Lavier et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Josefa González et al.   PLoS Genetics

Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs

(2009) E Lerat   HEREDITY

Characterizing natural variation using next-generation sequencing technologies

(2009) Yoav Gilad et al.   TRENDS IN GENETICS

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

A universal classification of eukaryotic transposable elements implemented in Repbase

(2008) Vladimir V. Kapitonov et al.   NATURE REVIEWS GENETICS

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

(2008) Josefa González et al.   PLOS BIOLOGY