Transposable element annotation in non‐model species: The benefits of species‐specific repeat libraries using semi‐automated EDTA and DeepTE de novo pipelines

Genomes of the willow-galling sawflies Euura lappo and Eupontania aestiva (Hymenoptera: Tenthredinidae): a resource for research on ecological speciation, adaptation, and gall induction

(2021) Craig Michell et al.   G3-Genes Genomes Genetics

DeepTE: a computational method for de novo classification of transposons with convolutional neural network

(2020) Haidong Yan et al.   BIOINFORMATICS

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Measuring and interpreting transposable element expression

(2020) Sophie Lanciano et al.   NATURE REVIEWS GENETICS

A Field Guide to Eukaryotic Transposable Elements

(2020) Jonathan N. Wells et al.   Annual Review of Genetics

The Piranha Genome Provides Molecular Insight Associated to Its Unique Feeding Behavior

(2019) Manfred Schartl et al.   Genome Biology and Evolution

Evolution and diversity of transposable elements in fish genomes

(2019) Feng Shao et al.   Scientific Reports

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Evolution and Diversity of Transposable Elements in Vertebrate Genomes

(2017) Cibele G. Sotero-Caio et al.   Genome Biology and Evolution

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Transposable elements: Self-seekers of the germline, team-players of the soma

(2016) David Haig   BIOESSAYS

Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies

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

TransRate: reference-free quality assessment of de novo transcriptome assemblies

(2016) Richard Smith-Unna et al.   GENOME RESEARCH

Horizontal Transfer Can Drive a Greater Transposable Element Load in Large Populations

(2016) Sam B. Groth et al.   JOURNAL OF HEREDITY

Discovery of Novel Genes Derived from Transposable Elements Using Integrative Genomic Analysis

(2015) Douglas R. Hoen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries

(2013) Richard M. Leggett et al.   BIOINFORMATICS

EVOLUTIONARY ORIGIN AND EARLY BIOGEOGRAPHY OF OTOPHYSAN FISHES (OSTARIOPHYSI: TELEOSTEI)

(2013) Wei-Jen Chen et al.   EVOLUTION

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

Transposable Elements Re-Wire and Fine-Tune the Transcriptome

(2013) Michael Cowley et al.   PLoS Genetics

An automated homology-based approach for identifying transposable elements

(2011) Ryan C Kennedy et al.   BMC BIOINFORMATICS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Competition and phylogeny determine community structure in Müllerian co-mimics

(2010) Markos A. Alexandrou et al.   NATURE

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

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS