Transposable Elements Are Important Contributors to Standing Variation in Gene Expression in Capsella Grandiflora

Conserved Noncoding Elements Influence the Transposable Element Landscape in Drosophila

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

Dysregulation of expression correlates with rare-allele burden and fitness loss in maize

(2018) Karl A. G. Kremling et al.   NATURE

The Role of Small RNA-Based Epigenetic Silencing for Purifying Selection on Transposable Elements in Capsella grandiflora

(2017) Robert Horvath et al.   Genome Biology and Evolution

The Relationship between Selection, Network Connectivity, and Regulatory Variation within a Population of Capsella grandiflora

(2017) Emily B. Josephs et al.   Genome Biology and Evolution

Natural Variation in the Distribution and Abundance of Transposable Elements Across the Caenorhabditis elegans Species

(2017) K.M. Laricchia et al.   MOLECULAR BIOLOGY AND EVOLUTION

Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators

(2017) Nian Liu et al.   NATURE

The impact of rare variation on gene expression across tissues

(2017) Xin Li et al.   NATURE

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

The impact of structural variation on human gene expression

(2017) Colby Chiang et al.   NATURE GENETICS

Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution

(2017) Yuh Chwen G Lee et al.   eLife

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

(2017) Jinfeng Chen et al.   PeerJ

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

Contrasting Frequencies and Effects ofcis- andtrans-Regulatory Mutations Affecting Gene Expression

(2016) Brian P. H. Metzger et al.   MOLECULAR BIOLOGY AND EVOLUTION

The industrial melanism mutation in British peppered moths is a transposable element

(2016) Arjen E. van’t Hof et al.   NATURE

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

The Arabidopsis thaliana mobilome and its impact at the species level

(2016) Leandro Quadrana et al.   eLife

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

(2016) Tim Stuart et al.   eLife

Association mapping reveals the role of purifying selection in the maintenance of genomic variation in gene expression

(2015) Emily B. Josephs et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhancer Runaway and the Evolution of Diploid Gene Expression

(2015) Frédéric Fyon et al.   PLoS Genetics

Transposable element detection from whole genome sequence data

(2015) Adam D. Ewing   Mobile DNA

The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes

(2014) Jeffrey L. Bennetzen et al.   Annual Review of Plant Biology

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Gene Expression Variation in Drosophila melanogaster Due to Rare Transposable Element Insertion Alleles of Large Effect

(2014) J. M. Cridland et al.   GENETICS

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

Evidence for Widespread Positive and Negative Selection in Coding and Conserved Noncoding Regions of Capsella grandiflora

(2014) Robert J. Williamson et al.   PLoS Genetics

Genome-Wide Association Study of Extreme Longevity in Drosophila melanogaster

(2013) Molly K. Burke et al.   Genome Biology and Evolution

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

(2013) A. Battle et al.   GENOME RESEARCH

Abundance and Distribution of Transposable Elements in Two Drosophila QTL Mapping Resources

(2013) Julie M. Cridland et al.   MOLECULAR BIOLOGY AND EVOLUTION

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

(2013) Annabelle Haudry et al.   NATURE GENETICS

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

(2013) Tanja Slotte et al.   NATURE GENETICS

Genomic Identification of Founding Haplotypes Reveals the History of the Selfing Species Capsella rubella

(2013) Yaniv Brandvain et al.   PLoS Genetics

Transposon Variants and Their Effects on Gene Expression in Arabidopsis

(2013) Xi Wang et al.   PLoS Genetics

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Genome-Wide Characterization of Nonreference Transposons Reveals Evolutionary Propensities of Transposons in Soybean

(2012) Z. Tian et al.   PLANT CELL

Retrotransposons Control Fruit-Specific, Cold-Dependent Accumulation of Anthocyanins in Blood Oranges

(2012) E. Butelli et al.   PLANT CELL

Transposable Elements Are a Major Cause of Somatic Polymorphism in Vitis vinifera L.

(2012) Grégory Carrier et al.   PLoS One

Genomic Variation and Its Impact on Gene Expression in Drosophila melanogaster

(2012) Andreas Massouras et al.   PLoS Genetics

GENETIC ARCHITECTURE AND ADAPTIVE SIGNIFICANCE OF THE SELFING SYNDROME INCAPSELLA

(2011) Tanja Slotte et al.   EVOLUTION

Convergent Evolution of Endometrial Prolactin Expression in Primates, Mice, and Elephants Through the Independent Recruitment of Transposable Elements

(2011) Deena Emera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems

(2011) KATE R. ST. ONGE et al.   MOLECULAR ECOLOGY

Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis

(2011) Ikhlak Ahmed et al.   NUCLEIC ACIDS RESEARCH

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

Rare and Common Regulatory Variation in Population-Scale Sequenced Human Genomes

(2011) Stephen B. Montgomery et al.   PLoS Genetics

The Evolution and Diversity of DNA Transposons in the Genome of the Lizard Anolis carolinensis

(2010) Peter A. Novick et al.   Genome Biology and Evolution

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Genome-Wide Evidence for Efficient Positive and Purifying Selection in Capsella grandiflora, a Plant Species with a Large Effective Population Size

(2010) T. Slotte et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Recent speciation associated with the evolution of selfing in Capsella

(2009) J. P. Foxe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High Rate of Recent Transposable Element–Induced Adaptation in Drosophila melanogaster

(2008) Josefa González et al.   PLOS BIOLOGY