A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore

A behavior-manipulating virus relative as a source of adaptive genes for Drosophila parasitoids

(2020) D Di Giovanni et al.   MOLECULAR BIOLOGY AND EVOLUTION

Viral infection impacts transposable element transcript amounts in Drosophila

(2020) Marlène Roy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamics of Transposable Element Invasions with piRNA Clusters

(2019) Robert Kofler   MOLECULAR BIOLOGY AND EVOLUTION

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Scaling read aligners to hundreds of threads on general-purpose processors

(2018) Ben Langmead et al.   BIOINFORMATICS

Long reads: their purpose and place

(2018) Martin O Pollard et al.   HUMAN MOLECULAR GENETICS

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing

(2018) Edwin A. Solares et al.   G3-Genes Genomes Genetics

D-GENIES: dot plot large genomes in an interactive, efficient and simple way

(2018) Floréal Cabanettes et al.   PeerJ

The somatic piRNA pathway controls germline transposition over generations

(2018) Bridlin Barckmann et al.   NUCLEIC ACIDS RESEARCH

Population-specific dynamics and selection patterns of transposable element insertions in European natural populations

(2018) Emmanuelle Lerat et al.   MOLECULAR ECOLOGY

Hidden genetic variation shapes the structure of functional elements in Drosophila

(2017) Mahul Chakraborty et al.   NATURE GENETICS

Resolving the prevalence of somatic transposition in Drosophila

(2017) Christoph D Treiber et al.   eLife

DrosophilaFemales Undergo Genome Expansion after Interspecific Hybridization

(2016) Valèria Romero-Soriano et al.   Genome Biology and Evolution

PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq

(2016) Robert Kofler et al.   MOLECULAR BIOLOGY AND EVOLUTION

TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes

(2016) Emmanuelle Lerat et al.   NUCLEIC ACIDS RESEARCH

P elements and the determinants of hybrid dysgenesis have different dynamics of propagation in Drosophila melanogaster populations

(2015) Olesia M. Ignatenko et al.   GENETICA

De Novo Assembly and Annotation of the Asian Tiger Mosquito (Aedes albopictus) Repeatome with dnaPipeTE from Raw Genomic Reads and Comparative Analysis with the Yellow Fever Mosquito (Aedes aegypti)

(2015) Clément Goubert et al.   Genome Biology and Evolution

Unique transposon landscapes are pervasive acrossDrosophila melanogastergenomes

(2015) Reazur Rahman et al.   NUCLEIC ACIDS RESEARCH

The Dfam database of repetitive DNA families

(2015) Robert Hubley et al.   NUCLEIC ACIDS RESEARCH

Increased production of piRNAs from euchromatic clusters and genes in Anopheles gambiae compared with Drosophila melanogaster

(2015) Phillip George et al.   Epigenetics & Chromatin

Tempo and Mode of Transposable Element Activity in Drosophila

(2015) Robert Kofler et al.   PLoS Genetics

Transcriptional properties and splicing of the flamenco piRNA cluster

(2014) C. Goriaux et al.   EMBO REPORTS

Variation in piRNA and Transposable Element Content in Strains of Drosophila melanogaster

(2014) Jimin Song et al.   Genome Biology and Evolution

P element activity and molecular structure in Drosophila melanogaster populations from Firtina Valley, Turkey

(2014) Banu Sebnem Onder et al.   JOURNAL OF INSECT SCIENCE

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

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

(2014) Anna-Sophie Fiston-Lavier et al.   NUCLEIC ACIDS RESEARCH

FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations

(2014) G. dos Santos et al.   NUCLEIC ACIDS RESEARCH

Euchromatic Transposon Insertions Trigger Production of Novel Pi- and Endo-siRNAs at the Target Sites in the Drosophila Germline

(2014) Sergey Shpiz et al.   PLoS Genetics

Analysis of piRNA-Mediated Silencing of Active TEs in Drosophila melanogaster Suggests Limits on the Evolution of Host Genome Defense

(2013) Erin S. Kelleher et al.   MOLECULAR BIOLOGY AND EVOLUTION

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters

(2013) V. Zanni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

piRNA-mediated transgenerational inheritance of an acquired trait

(2012) T. Grentzinger et al.   GENOME RESEARCH

A comparative analysis of the amounts and dynamics of transposable elements in natural populations of Drosophila melanogaster and Drosophila simulans

(2012) Cristina Vieira et al.   JOURNAL OF ENVIRONMENTAL RADIOACTIVITY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

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

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

(2010) Petr Novák et al.   BMC BIOINFORMATICS

Comparative analysis of transposable elements in the melanogaster subgroup sequenced genomes

(2010) Emmanuelle Lerat et al.   GENE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The evolutionary dynamics of the Helena retrotransposon revealed by sequenced Drosophila genomes

(2009) Adriana Granzotto et al.   BMC EVOLUTIONARY BIOLOGY

Genomic distribution of retrotransposons 297, 1731, copia, mdg1 and roo in the Drosophila melanogaster species subgroup

(2009) Julia Díaz-González et al.   GENETICA

Losing helena: The extinction of a drosophila line-like element

(2008) Rita Rebollo et al.   BMC GENOMICS

A universal classification of eukaryotic transposable elements implemented in Repbase

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