Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA

Mouse germ line mutations due to retrotransposon insertions

(2019) Liane Gagnier et al.   Mobile DNA

Transposition favors the generation of large effect mutations that may facilitate rapid adaption

(2019) Leandro Quadrana et al.   Nature Communications

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Sequence-Independent Identification of Active LTR Retrotransposons in Arabidopsis

(2018) Jayne Griffiths et al.   Molecular Plant

Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis

(2018) Filipe Borges et al.   NATURE GENETICS

Accurate detection of complex structural variations using single-molecule sequencing

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

Tie-Break: Host and Retrotransposons Play tRNA

(2018) Andrea J. Schorn et al.   TRENDS IN CELL BIOLOGY

piRNA-Guided Genome Defense: From Biogenesis to Silencing

(2018) Benjamin Czech et al.   Annual Review of Genetics

Live-cell analysis of DNA methylation during sexual reproduction inArabidopsisreveals context and sex-specific dynamics controlled by noncanonical RdDM

(2017) Mathieu Ingouff et al.   GENES & DEVELOPMENT

A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements

(2017) Stefan Oberlin et al.   GENOME RESEARCH

piRNA-mediated regulation of transposon alternative splicing in the soma and germ line

(2017) Felipe Karam Teixeira et al.   NATURE

A single miR390 targeting event is sufficient for triggering TAS3-tasiRNA biogenesis in Arabidopsis

(2017) Felipe Fenselau de Felippes et al.   NUCLEIC ACIDS RESEARCH

Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants

(2017) Sophie Lanciano et al.   PLoS Genetics

systemPipeR: NGS workflow and report generation environment

(2016) Tyler W. H. Backman et al.   BMC BIOINFORMATICS

The Slicer Activity of ARGONAUTE1 is Required Specifically for the Phasing, Not Production, of Trans-Acting Short Interfering RNAs in Arabidopsis

(2016) Laura Arribas-Hernández et al.   PLANT CELL

Determinants of Genomic RNA Encapsidation in the Saccharomyces cerevisiae Long Terminal Repeat Retrotransposons Ty1 and Ty3

(2016) Katarzyna Pachulska-Wieczorek et al.   Viruses-Basel

Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

(2016) Tim Stuart et al.   eLife

The expanding world of small RNAs in plants

(2015) Filipe Borges et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNAi and Heterochromatin Assembly

(2015) Robert Martienssen et al.   Cold Spring Harbor Perspectives in Biology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis

(2014) Kate M. Creasey et al.   NATURE

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle

(2014) W. Wang et al.   Nature Communications

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

MicroRNAs Inhibit the Translation of Target mRNAs on the Endoplasmic Reticulum in Arabidopsis

(2013) Shengben Li et al.   CELL

Parent-of-origin control of transgenerational retrotransposon proliferation in Arabidopsis

(2013) Jon Reinders et al.   EMBO REPORTS

Reconstructing de novo silencing of an active plant retrotransposon

(2013) Arturo Marí-Ordóñez et al.   NATURE GENETICS

The Initiation of Epigenetic Silencing of Active Transposable Elements Is Triggered by RDR6 and 21-22 Nucleotide Small Interfering RNAs

(2013) S. Nuthikattu et al.   PLANT PHYSIOLOGY

BARE Retrotransposons Are Translated and Replicated via Distinct RNA Pools

(2013) Wei Chang et al.   PLoS One

Quantitatively Increased Somatic Transposition of Transposable Elements in Drosophila Strains Compromised for RNAi

(2013) Weiwu Xie et al.   PLoS One

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

(2013) P. Juntawong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative analysis of the time-course of viral DNA forms during the HIV-1 life cycle

(2013) Soundasse Munir et al.   Retrovirology

ShortStack: Comprehensive annotation and quantification of small RNA genes

(2013) M. J. Axtell   RNA

Active Transposition in Genomes

(2012) Cheng Ran Lisa Huang et al.   Annual Review of Genetics

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Retrotransposons

(2012) David J. Finnegan   CURRENT BIOLOGY

Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint

(2012) Sam Guoping Gu et al.   NATURE GENETICS

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao et al.   GENOME BIOLOGY

High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis

(2011) N. W. Breakfield et al.   GENOME RESEARCH

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress

(2011) Hidetaka Ito et al.   NATURE

The role of unintegrated DNA in HIV infection

(2011) Richard D Sloan et al.   Retrovirology

The HIV-1 Central Polypurine Tract Functions as a Second Line of Defense against APOBEC3G/F

(2010) C. Hu et al.   JOURNAL OF VIROLOGY

miR390,Arabidopsis TAS3tasiRNAs, and TheirAUXIN RESPONSE FACTORTargets Define an Autoregulatory Network Quantitatively Regulating Lateral Root Growth

(2010) Elena Marin et al.   PLANT CELL

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana

(2009) Robert Grant-Downton et al.   BMC GENOMICS

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

Bursts of retrotransposition reproduced in Arabidopsis

(2009) Sayuri Tsukahara et al.   NATURE

Selective epigenetic control of retrotransposition in Arabidopsis

(2009) Marie Mirouze et al.   NATURE

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila

(2009) Delphine Fagegaltier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

How Athila retrotransposons survive in the Arabidopsis genome

(2008) Antonio Marco et al.   BMC GENOMICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY