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

A Burden of Rare Variants Associated with Extremes of Gene Expression in Human Peripheral Blood

(2016) Jing Zhao et al.   AMERICAN JOURNAL OF HUMAN GENETICS

On the origin and evolutionary consequences of gene body DNA methylation

(2016) Adam J. Bewick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Arabidopsis thaliana mobilome and its impact at the species level

(2016) Leandro Quadrana et al.   eLife

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

(2015) Irina Makarevitch et al.   PLoS Genetics

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

The bright side of transposons in crop evolution

(2014) C. Vitte et al.   Briefings in Functional Genomics

Environmentally responsive genome-wide accumulation of de novoArabidopsis thalianamutations and epimutations

(2014) Caifu Jiang et al.   GENOME RESEARCH

Hi-C Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila

(2014) Stefan Grob et al.   MOLECULAR CELL

The genome of the stress-tolerant wild tomato species Solanum pennellii

(2014) Anthony Bolger et al.   NATURE GENETICS

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

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

Extensive amplification of the E2F transcription factor binding sites by transposons during evolution ofBrassicaspecies

(2014) Elizabeth Hénaff et al.   PLANT JOURNAL

Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana

(2014) Alessandra M. Sullivan et al.   Cell Reports

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

RSVSim: an R/Bioconductor package for the simulation of structural variations

(2013) C. Bartenhagen et al.   BIOINFORMATICS

The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin

(2013) Assaf Zemach et al.   CELL

Patterns of population epigenomic diversity

(2013) Robert J. Schmitz et al.   NATURE

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

YAHA: fast and flexible long-read alignment with optimal breakpoint detection

(2012) G. G. Faust et al.   BIOINFORMATICS

Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel

(2012) Matthew W Horton et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress

(2011) Hidetaka Ito et al.   NATURE

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Reference-guided assembly of four diverse Arabidopsis thaliana genomes

(2011) K. Schneeberger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Selective epigenetic control of retrotransposition in Arabidopsis

(2009) Marie Mirouze et al.   NATURE

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

(2008) Ryan Lister et al.   CELL

Many or most genes in Arabidopsis transposed after the origin of the order Brassicales

(2008) M. Freeling et al.   GENOME RESEARCH

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

A Genome-Wide Functional Investigation into the Roles of Receptor-Like Proteins in Arabidopsis

(2008) G. Wang et al.   PLANT PHYSIOLOGY