Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast

Structural basis of Ty1 integrase tethering to RNA polymerase III for targeted retrotransposon integration

(2023) Phong Quoc Nguyen et al.   Nature Communications

Paths to adaptation under fluctuating nitrogen starvation: The spectrum of adaptive mutations in Saccharomyces cerevisiae is shaped by retrotransposons and microhomology-mediated recombination

(2023) Michelle Hays et al.   PLoS Genetics

Epistatic selection on a selfish Segregation Distorter supergene – drive, recombination, and genetic load

(2022) Beatriz Navarro-Dominguez et al.   eLife

Ongoing transposition in cell culture reveals the phylogeny of diverse Drosophila S2 sublines

(2022) Shunhua Han et al.   GENETICS

Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line

(2022) Shunhua Han et al.   NUCLEIC ACIDS RESEARCH

Bergerac strains of Caenorhabditis elegans revisited: expansion of Tc1 elements imposes a significant genomic and fitness cost

(2022) Austin T Daigle et al.   G3-Genes Genomes Genetics

yEvo: experimental evolution in high school classrooms selects for novel mutations that impact clotrimazole resistance in Saccharomyces cerevisiae

(2022) Matthew Bryce Taylor et al.   G3-Genes Genomes Genetics

Multiple origins, one evolutionary trajectory: gradual evolution characterizes distinct lineages of allotetraploid Brachypodium

(2022) Virginia T Scarlett et al.   GENETICS

Stage-specific transposon activity in the life cycle of the fairy-ring mushroom Marasmius oreades

(2022) Markus Hiltunen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Light and shadow on the mechanisms of integration site selection in yeast Ty retrotransposon families

(2021) Amandine Bonnet et al.   CURRENT GENETICS

A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies

(2021) Tianxiong Yu et al.   NUCLEIC ACIDS RESEARCH

Asexual Experimental Evolution of Yeast Does Not Curtail Transposable Elements

(2021) Piaopiao Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Species-Wide Transposable Element Repertoires Retrace the Evolutionary History of the Saccharomyces cerevisiae Host

(2021) Claudine Bleykasten-Grosshans et al.   MOLECULAR BIOLOGY AND EVOLUTION

Towards population-scale long-read sequencing

(2021) Wouter De Coster et al.   NATURE REVIEWS GENETICS

A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen

(2021) Ursula Oggenfuss et al.   eLife

Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture

(2021) Shunhua Han et al.   GENETICS

TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation

(2021) et al.   Mobile DNA

Transposon activation is a major driver in the genome evolution of cultivated olive trees ( Olea europaea L.)

(2020) Jaime Jiménez‐Ruiz et al.   Plant Genome

Various modes of HP1a interactions with the euchromatic chromosome arms in Drosophila ovarian somatic cells

(2020) Artem A. Ilyin et al.   CHROMOSOMA

A small targeting domain in Ty1 integrase is sufficient to direct retrotransposon integration upstream of tRNA genes

(2020) Amna Asif‐Laidin et al.   EMBO JOURNAL

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

(2020) Valentina Peona et al.   Molecular Ecology Resources

Devia TE : Assembly‐free analysis and visualization of mobile genetic element composition

(2019) Lukas Weilguny et al.   Molecular Ecology Resources

Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites

(2019) Kurt Patterson et al.   GENOME RESEARCH

Asexual reproduction reduces transposable element load in experimental yeast populations

(2019) Jens Bast et al.   eLife

Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome

(2019) Elisa Oberbeckmann et al.   GENOME RESEARCH

Nuclear Ccr4-Not mediates the degradation of telomeric and transposon transcripts at chromatin in the Drosophila germline

(2019) Maria Kordyukova et al.   NUCLEIC ACIDS RESEARCH

A benchmark of transposon insertion detection tools using real data

(2019) Pol Vendrell-Mir et al.   Mobile DNA

panISa: Ab initio detection of insertion sequences in bacterial genomes from short read sequence data

(2018) Panisa Treepong et al.   BIOINFORMATICS

Conserved Noncoding Elements Influence the Transposable Element Landscape in Drosophila

(2018) Manee M Manee et al.   Genome Biology and Evolution

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis

(2018) Stephanie N. Schauer et al.   GENOME RESEARCH

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

(2018) Jackson Peter et al.   NATURE

Genome-Wide Estimates of Transposable Element Insertion and Deletion Rates in Drosophila Melanogaster

(2017) Jeffrey R. Adrion et al.   Genome Biology and Evolution

The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology

(2017) Eugene J. Gardner et al.   GENOME RESEARCH

Piwi interacts with chromatin at nuclear pores and promiscuously binds nuclear transcripts in Drosophila ovarian somatic cells

(2017) Artem A. Ilyin et al.   NUCLEIC ACIDS RESEARCH

Sex Chromosome Evolution, Heterochiasmy, and Physiological QTL in the Salmonid Brook Charr Salvelinus fontinalis

(2017) Ben J.G. Sutherland et al.   G3-Genes Genomes Genetics

RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing

(2017) Jinfeng Chen et al.   PeerJ

Genomic analysis of P elements in natural populations of Drosophila melanogaster

(2017) Casey M. Bergman et al.   PeerJ

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Benchmarking computational tools for polymorphic transposable element detection

(2016) Lavanya Rishishwar et al.   BRIEFINGS IN BIOINFORMATICS

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

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

The 100-genomes strains, anS. cerevisiaeresource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen

(2015) Pooja K. Strope et al.   GENOME RESEARCH

An RNA polymerase III subunit determines sites of retrotransposon integration

(2015) A. Bridier-Nahmias et al.   SCIENCE

Transposable element detection from whole genome sequence data

(2015) Adam D. Ewing   Mobile DNA

bwtool: a tool for bigWig files

(2014) Andy Pohl et al.   BIOINFORMATICS

Comparative analysis of methods for genome-wide nucleosome cartography

(2014) Luis Quintales et al.   BRIEFINGS IN BIOINFORMATICS

UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

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

(2014) Jiali Zhuang et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analysis of intraspecific transposon diversity in yeast

(2013) Claudine Bleykasten-Grosshans et al.   BMC GENOMICS

Mobile element biology: new possibilities with high-throughput sequencing

(2013) Jinchuan Xing et al.   TRENDS IN 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

RetroSeq: transposable element discovery from next-generation sequencing data

(2012) Thomas M. Keane et al.   BIOINFORMATICS

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

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

(2012) L. Mularoni et al.   GENOME RESEARCH

Retrotransposon profiling of RNA polymerase III initiation sites

(2012) X. Qi 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

Two large-scale analyses of Ty1 LTR-retrotransposon de novo insertion events indicate that Ty1 targets nucleosomal DNA near the H2A/H2B interface

(2012) Antoine Bridier-Nahmias et al.   Mobile DNA

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Reading TE leaves: New approaches to the identification of transposable element insertions

(2011) D. A. Ray et al.   GENOME RESEARCH

The self-assessment trap: can we all be better than average?

(2011) R. Norel et al.   Molecular Systems Biology

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences

(2008) Surya Saha et al.   Tropical Plant Biology