A Genomic Survey of Mayetiola destructor Mobilome Provides New Insights into the Evolutionary History of Transposable Elements in the Cecidomyiid Midges

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

The evolutionary history of mariner elements in stalk-eyed flies reveals the horizontal transfer of transposons from insects into the genome of the cnidarian Hydra vulgaris

(2020) C. Alastair Grace et al.   PLoS One

Twenty years of transposable element analysis in the Arabidopsis thaliana genome

(2020) Hadi Quesneville   Mobile DNA

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

(2020) Valentina Peona et al.   Molecular Ecology Resources

Screening of Helicoverpa armigera Mobilome Revealed Transposable Element Insertions in Insecticide Resistance Genes

(2020) Khouloud KLAI et al.   Insects

Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects

(2019) Malte Petersen et al.   BMC EVOLUTIONARY BIOLOGY

Birth, School, Work, Death, and Resurrection: The Life Stages and Dynamics of Transposable Element Proliferation

(2019) Justin P. Blumenstiel   Genes

Mammalian transposable elements and their impacts on genome evolution

(2018) Roy N. Platt et al.   CHROMOSOME RESEARCH

Exaptation of transposable element coding sequences

(2018) Zoé Joly-Lopez et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes

(2018) Juan Manuel Crescente et al.   BMC BIOINFORMATICS

Transposable elements in the Anopheles funestus transcriptome

(2017) Rita D. Fernández-Medina et al.   GENETICA

The distribution of transposable elements (TEs) in the promoter regions of moso bamboo genes and its influence on downstream genes

(2017) Mingbing Zhou et al.   TREES-STRUCTURE AND FUNCTION

Avirulence gene mapping in the Hessian fly ( Mayetiola destructor ) reveals a protein phosphatase 2C effector gene family

(2016) Chaoyang Zhao et al.   JOURNAL OF INSECT PHYSIOLOGY

PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq

(2016) Robert Kofler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Natural courtship song variation caused by an intronic retroelement in an ion channel gene

(2016) Yun Ding et al.   NATURE

Regulatory activities of transposable elements: from conflicts to benefits

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

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Do larger genomes contain more diverse transposable elements?

(2015) Tyler A Elliott et al.   BMC EVOLUTIONARY BIOLOGY

A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor

(2015) Chaoyang Zhao et al.   CURRENT BIOLOGY

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

A call for benchmarking transposable element annotation methods

(2015) Douglas R. Hoen et al.   Mobile DNA

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

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

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

Phylogenetic analysis of Maverick/Polinton giant transposons across organisms

(2014) Saija Haapa-Paananen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The i5k Workspace@NAL—enabling genomic data access, visualization and curation of arthropod genomes

(2014) Monica Poelchau et al.   NUCLEIC ACIDS RESEARCH

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Compact genome of the Antarctic midge is likely an adaptation to an extreme environment

(2014) Joanna L. Kelley et al.   Nature Communications

Horizontal transfer of transposons between and within crustaceans and insects

(2014) Mathilde Dupeyron et al.   Mobile DNA

Miniature inverted-repeat transposable elements: discovery, distribution, and activity

(2013) Isam Fattash et al.   GENOME

The impact of transposable elements in environmental adaptation

(2013) Elena Casacuberta et al.   MOLECULAR ECOLOGY

Web Apollo: a web-based genomic annotation editing platform

(2013) Eduardo Lee et al.   GENOME BIOLOGY

Gall Midges (Hessian Flies) as Plant Pathogens

(2012) Jeff J. Stuart et al.   Annual Review of Phytopathology

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Human Transposon Tectonics

(2012) Kathleen H. Burns et al.   CELL

The genome of flax (Linum usitatissimum) assembledde novofrom short shotgun sequence reads

(2012) Zhiwen Wang et al.   PLANT JOURNAL

C-GATE - catalogue of genes affected by transposable elements

(2012) Rita Rebollo et al.   Mobile DNA

The struggle for life of the genome's selfish architects

(2011) Aurélie Hua-Van et al.   Biology Direct

An automated homology-based approach for identifying transposable elements

(2011) Ryan C Kennedy et al.   BMC BIOINFORMATICS

Novel transposable elements from Anopheles gambiae

(2011) Rita D Fernández-Medina et al.   BMC GENOMICS

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(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Distributions of Transposable Elements Reveal Hazardous Zones in Mammalian Introns

(2011) Ying Zhang et al.   PLoS Computational Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genomic structures of Cyp9m10 in pyrethroid resistant and susceptible strains of Culex quinquefasciatus

(2010) Kentaro Itokawa et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Assessment of structural variation and molecular mapping of insertion sites ofDesmar-like elements in the Hessian fly genome

(2010) S. K. Behura et al.   INSECT MOLECULAR BIOLOGY

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Genome-Wide Patterns of Adaptation to Temperate Environments Associated with Transposable Elements in Drosophila

(2010) Josefa González et al.   PLoS Genetics

Non-long terminal repeat (non-LTR) retrotransposons: mechanisms, recent developments, and unanswered questions

(2010) Jeffrey S Han   Mobile DNA

Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs

(2009) E Lerat   HEREDITY

Tuned for Transposition: Molecular Determinants Underlying the Hyperactivity of a Stowaway MITE

(2009) G. Yang et al.   SCIENCE

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

(2008) Josefa González et al.   PLOS BIOLOGY