Recent and dynamic transposable elements contribute to genomic divergence under asexuality

Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants

(2016) Julie Ferreira de Carvalho et al.   BMC GENOMICS

Natural epigenetic variation contributes to heritable flowering divergence in a widespread asexual dandelion lineage

(2016) Rutger A. Wilschut et al.   MOLECULAR ECOLOGY

epiGBS: reference-free reduced representation bisulfite sequencing

(2016) Thomas P van Gurp et al.   NATURE METHODS

Evolutionary transitions in the Asteraceae coincide with marked shifts in transposable element abundance

(2015) S. Evan Staton et al.   BMC GENOMICS

Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm

(2015) Meilina Ong-Abdullah et al.   NATURE

Analysis of the giant genomes ofFritillaria(Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size

(2015) Laura J. Kelly et al.   NEW PHYTOLOGIST

Evolutionary dynamics of retrotransposons following autopolyploidy in the Buckler Mustard species complex

(2015) Amélie Bardil et al.   PLANT JOURNAL

A Cluster of Recently Inserted Transposable Elements Associated with siRNAs in

(2015) Lei Gong et al.   Plant Genome

ARGONAUTE 6 bridges transposable element mRNA-derived siRNAs to the establishment of DNA methylation

(2014) A. D. McCue et al.   EMBO JOURNAL

Bursts of transposable elements as an evolutionary driving force

(2014) A. Belyayev   JOURNAL OF EVOLUTIONARY BIOLOGY

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

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads

(2013) Lucia Natali et al.   BMC GENOMICS

Retrotransposon-related genetic distance and hybrid performance in sunflower (Helianthus annuus L.)

(2013) M. Buti et al.   EUPHYTICA

Transposable Elements: Powerful Contributors to Angiosperm Evolution and Diversity

(2013) Keith R. Oliver et al.   Genome Biology and Evolution

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

The Effects of Deleterious Mutations on Evolution at Linked Sites

(2012) Brian Charlesworth   GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

How important are transposons for plant evolution?

(2012) Damon Lisch   NATURE REVIEWS GENETICS

Polymorphism and methylation patterns in Agave tequilana Weber var. ‘Azul’ plants propagated asexually by three different methods

(2012) Miriam Díaz-Martínez et al.   PLANT SCIENCE

Widespread dynamic DNA methylation in response to biotic stress

(2012) R. H. Dowen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Repeat associated small RNAs vary among parents and following hybridization in maize

(2012) W. T. Barber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

(2012) Yaping Liu et al.   GENOME BIOLOGY

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

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata

(2010) Steven Lockton et al.   BMC EVOLUTIONARY BIOLOGY

GenBank

(2010) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Transposable elements in a marginal plant population: temporal fluctuations provide new insights into genome evolution of wild diploid wheat

(2010) Alexander Belyayev et al.   Mobile DNA

Transposable elements: powerful facilitators of evolution

(2009) Keith R. Oliver et al.   BIOESSAYS

Copia and Gypsy retrotransposons activity in sunflower (Helianthus annuus L.)

(2009) Marco Vukich et al.   BMC PLANT BIOLOGY

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

Stress-induced DNA methylation changes and their heritability in asexual dandelions

(2009) Koen J. F. Verhoeven et al.   NEW PHYTOLOGIST

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata

(2008) S. Lockton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA