Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants

Identification of Extrachromosomal Circular DNA in Hop via Rolling Circle Amplification

(2016) Alfredo Diaz-Lara et al.   CYTOGENETIC AND GENOME RESEARCH

Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution

(2015) Elizabeth Hénaff et al.   BMC GENOMICS

Ubiquitous L1 Mosaicism in Hippocampal Neurons

(2015) Kyle R. Upton et al.   CELL

Silencing of active transposable elements in plants

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

A Solution to the C-Value Paradox and the Function of Junk DNA: The Genome Balance Hypothesis

(2015) Michael Freeling et al.   Molecular Plant

Loss of function mutations in the rice chromomethylase OsCMT3a cause a burst of transposition

(2015) Chaoyang Cheng et al.   PLANT JOURNAL

Global Analysis Reveals the Crucial Roles of DNA Methylation during Rice Seed Development

(2015) Mei-Qing Xing et al.   PLANT PHYSIOLOGY

Extrachromosomal circular DNA is common in yeast

(2015) Henrik D. Møller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Production of Extrachromosomal MicroDNAs Is Linked to Mismatch Repair Pathways and Transcriptional Activity

(2015) Laura W. Dillon et al.   Cell Reports

Formation of Extrachromosomal Circular DNA from Long Terminal Repeats of Retrotransposons in Saccharomyces cerevisiae

(2015) Henrik D. Møller et al.   G3-Genes Genomes Genetics

Transposable element detection from whole genome sequence data

(2015) Adam D. Ewing   Mobile DNA

Genome-Wide Identification of New Reference Genes for qRT-PCR Normalization under High Temperature Stress in Rice Endosperm

(2015) Heng Xu et al.   PLoS One

A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data

(2014) David Coil et al.   BIOINFORMATICS

Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

(2014) Daniela Pignatta et al.   eLife

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

(2014) Steve Hoffmann et al.   GENOME BIOLOGY

Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm

(2013) J. A. Rodrigues et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes

(2012) Rita Rebollo et al.   Annual Review of Genetics

Epigenetic control of transposon transcription and mobility in Arabidopsis

(2012) Etienne Bucher et al.   CURRENT OPINION IN PLANT BIOLOGY

Developmental relaxation of transposable element silencing in plants: functional or byproduct?

(2012) Germán Martínez et al.   CURRENT OPINION IN PLANT BIOLOGY

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

Loss of DNA methylation affects the recombination landscape in Arabidopsis

(2012) M. Mirouze et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extrachromosomal MicroDNAs and Chromosomal Microdeletions in Normal Tissues

(2012) Y. Shibata et al.   SCIENCE

Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes

(2012) C. A. Ibarra et al.   SCIENCE

A Mechanism of Gene Amplification Driven by Small DNA Fragments

(2012) Kuntal Mukherjee et al.   PLoS Genetics

Somatic retrotransposition alters the genetic landscape of the human brain

(2011) J. Kenneth Baillie et al.   NATURE

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress

(2011) Hidetaka Ito et al.   NATURE

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

(2011) Vincent J Lynch et al.   NATURE GENETICS

Transpositional landscape of the rice genome revealed by paired-end mapping of high-throughput re-sequencing data

(2011) François Sabot et al.   PLANT JOURNAL

A Genome-Wide Survey of Imprinted Genes in Rice Seeds Reveals Imprinting Primarily Occurs in the Endosperm

(2011) Ming Luo et al.   PLoS Genetics

Local DNA hypomethylation activates genes in rice endosperm

(2010) A. Zemach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

Extrachromosomal Circular DNA in Eukaryotes: Possible Involvement in the Plasticity of Tandem Repeats

(2009) S. Cohen et al.   CYTOGENETIC AND GENOME RESEARCH

Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes

(2009) J. Reinders et al.   GENES & DEVELOPMENT

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Unexpected consequences of a sudden and massive transposon amplification on rice gene expression

(2009) Ken Naito et al.   NATURE

A transposon-induced epigenetic change leads to sex determination in melon

(2009) Antoine Martin et al.   NATURE

Selective epigenetic control of retrotransposition in Arabidopsis

(2009) Marie Mirouze et al.   NATURE

Identification of an active LTR retrotransposon in rice

(2009) Nathalie Picault et al.   PLANT JOURNAL

Genome-Wide Demethylation of Arabidopsis Endosperm

(2009) T.-F. Hsieh et al.   SCIENCE