Non-canonical Helitrons in Fusarium oxysporum

Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes

(2016) Nuria Rius et al.   BMC GENOMICS

Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies

(2016) Roy N. Platt et al.   Genome Biology and Evolution

Rolling-circle amplification of centromericHelitronsin plant genomes

(2016) Wenwei Xiong et al.   PLANT JOURNAL

A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes

(2016) Ivana Grabundzija et al.   Nature Communications

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

(2016) Henrik D. Møller et al.   Jove-Journal of Visualized Experiments

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

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi

(2014) Raúl Castanera et al.   BMC GENOMICS

Rolling-Circle Transposons Catalyze Genomic Innovation in a Mammalian Lineage

(2014) Jainy Thomas et al.   Genome Biology and Evolution

HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes

(2014) W. Xiong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DINE-1, the highest copy number repeats in Drosophila melanogaster are non-autonomous endonuclease-encoding rolling-circle transposable elements (Helentrons)

(2014) Jainy Thomas et al.   Mobile DNA

FusariumPathogenomics

(2013) Li-Jun Ma et al.   Annual Review of Microbiology

MITEs in the promoters of effector genes allow prediction of novel virulence genes in Fusarium oxysporum

(2013) Sarah M Schmidt et al.   BMC GENOMICS

Identification and Evolution of the Silkworm Helitrons and their Contribution to Transcripts

(2013) M.-J. Han et al.   DNA RESEARCH

New insights into helitron transposable elements in the mesopolyploid species Brassica rapa

(2013) Donghui Fu et al.   GENE

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements

(2013) Weidong Bao et al.   Mobile DNA

The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens

(2012) Daniel Croll et al.   PLoS Pathogens

Genomic impact of eukaryotic transposable elements

(2012) Irina R Arkhipova et al.   Mobile DNA

Structural characterization of helitrons and their stepwise capturing of gene fragments in the maize genome

(2011) Yongbin Dong et al.   BMC GENOMICS

Gene Capture by Helitron Transposons Reshuffles the Transcriptome of Maize

(2011) A. M. Barbaglia et al.   GENETICS

A Highly Conserved Effector in Fusarium oxysporum Is Required for Full Virulence on Arabidopsis

(2011) Louise F. Thatcher et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Next Generation Sequencing Provides Rapid Access to the Genome of Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust

(2011) Dario Cantu et al.   PLoS One

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

SF1 and SF2 helicases: family matters

(2010) Margaret E Fairman-Williams et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage

(2010) S. Raffaele et al.   SCIENCE

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution

(2010) Sarah Schaack et al.   TRENDS IN ECOLOGY & EVOLUTION

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Fragments of the key flowering gene GIGANTEA are associated with helitron-type sequences in the Pooideae grass Lolium perenne

(2009) Tim Langdon et al.   BMC PLANT BIOLOGY

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

(2009) Brian J. Haas et al.   NATURE

A cornucopia of Helitrons shapes the maize genome

(2009) C. Feschotte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure-based discovery and description of plant and animal Helitrons

(2009) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distribution, diversity, evolution, and survival of Helitrons in the maize genome

(2009) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamics of transposable elements: towards a community ecology of the genome

(2009) Samuel Venner et al.   TRENDS IN GENETICS

The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion

(2009) Jeffrey J. Coleman et al.   PLoS Genetics

RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences

(2008) James K Hane et al.   BMC BIOINFORMATICS

Computational prediction and molecular confirmation of Helitron transposons in the maize genome

(2008) Chunguang Du et al.   BMC GENOMICS

A comparative computational analysis of nonautonomous Helitron elements between maize and rice

(2008) Michael Sweredoski et al.   BMC GENOMICS

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE