Considerations and complications of mapping small RNA high-throughput data to transposable elements

Mechanistic and evolutionary questions about epigenetic conflicts between transposable elements and their plant hosts

(2016) Alexandros Bousios et al.   CURRENT OPINION IN PLANT BIOLOGY

Improved Placement of Multi-mapping Small RNAs

(2016) Nathan R. Johnson et al.   G3-Genes Genomes Genetics

A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis

(2015) Jixian Zhai et al.   CELL

Silencing of active transposable elements in plants

(2015) Dalen Fultz et al.   CURRENT OPINION IN PLANT BIOLOGY

A role for palindromic structures in the cis -region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response

(2015) Alexandros Bousios et al.   GENOME RESEARCH

The expanding world of small RNAs in plants

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

sRNAtoolbox: an integrated collection of small RNA research tools

(2015) Antonio Rueda et al.   NUCLEIC ACIDS RESEARCH

A Cluster of Recently Inserted Transposable Elements Associated with siRNAs in

(2015) Lei Gong et al.   Plant Genome

A comparison of performance of plant miRNA target prediction tools and the characterization of features for genome-wide target prediction

(2014) Prashant K Srivastava et al.   BMC GENOMICS

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

(2014) Marjori A. Matzke et al.   NATURE REVIEWS GENETICS

Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana

(2014) Florian Maumus et al.   Nature Communications

Three Groups of Transposable Elements with Contrasting Copy Number Dynamics and Host Responses in the Maize (Zea mays ssp. mays) Genome

(2014) Concepcion M. Diez et al.   PLoS Genetics

Classification and Comparison of Small RNAs from Plants

(2013) Michael J. Axtell   Annual Review of Plant Biology

ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data

(2013) Guan-Zheng Luo et al.   BIOINFORMATICS

isomiRex: Web-based identification of microRNAs, isomiR variations and differential expression using next-generation sequencing datasets

(2013) Gaurav Sablok et al.   FEBS LETTERS

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

(2013) M. Regulski et al.   GENOME RESEARCH

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1

(2013) Julie A. Law et al.   NATURE

RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond

(2013) Stephane E. Castel et al.   NATURE REVIEWS GENETICS

Genome-wide identification of genes regulated intransby transposable element small interfering RNAs

(2013) Andrea D McCue et al.   RNA Biology

ShortStack: Comprehensive annotation and quantification of small RNA genes

(2013) M. J. Axtell   RNA

Arguments for standardizing transposable element annotation in plant genomes

(2013) Raja Ragupathy et al.   TRENDS IN PLANT SCIENCE

The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets

(2012) M. B. Stocks et al.   BIOINFORMATICS

MASiVEdb: the Sirevirus Plant Retrotransposon Database

(2012) Alexandros Bousios et al.   BMC GENOMICS

CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize

(2012) J. I. Gent et al.   GENOME RESEARCH

Cytoplasmic Assembly and Selective Nuclear Import of Arabidopsis ARGONAUTE4/siRNA Complexes

(2012) Ruiqiang Ye et al.   MOLECULAR CELL

Reference genome sequence of the model plant Setaria

(2012) Jeffrey L Bennetzen et al.   NATURE BIOTECHNOLOGY

miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data

(2012) Jiyuan An et al.   NUCLEIC ACIDS RESEARCH

Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis

(2012) Yue Li et al.   NUCLEIC ACIDS RESEARCH

Evaluation of normalization methods in mammalian microRNA-Seq data

(2012) L. X. Garmire et al.   RNA

Identifying small interfering RNA loci from high-throughput sequencing data

(2011) Thomas J. Hardcastle et al.   BIOINFORMATICS

Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxurians

(2011) Maud I. Tenaillon et al.   Genome Biology and Evolution

miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments

(2011) M. Hackenberg et al.   NUCLEIC ACIDS RESEARCH

The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story

(2011) Alexandros Bousios et al.   PLANT JOURNAL

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

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

MASiVE: Mapping and Analysis of SireVirus Elements in plant genome sequences

(2010) N. Darzentas et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Finding sRNA generative locales from high-throughput sequencing data with NiBLS

(2010) Daniel MacLean et al.   BMC BIOINFORMATICS

Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: the key for their pattern of distribution within and across plants?

(2010) Alexandros Bousios et al.   BMC GENOMICS

The genome of woodland strawberry (Fragaria vesca)

(2010) Vladimir Shulaev et al.   NATURE GENETICS

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

mirTools: microRNA profiling and discovery based on high-throughput sequencing

(2010) Erle Zhu et al.   NUCLEIC ACIDS RESEARCH

A triptych of the evolution of plant transposable elements

(2010) Maud I. Tenaillon et al.   TRENDS IN PLANT SCIENCE

Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize

(2009) X. Wang et al.   PLANT CELL

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

(2009) Regina S. Baucom et al.   PLoS Genetics

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

A toolkit for analysing large-scale plant small RNA datasets

(2008) S. Moxon et al.   BIOINFORMATICS

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS