A call for benchmarking transposable element annotation methods

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

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

A new approach for annotation of transposable elements using small RNA mapping

(2015) Moaine El Baidouri et al.   NUCLEIC ACIDS RESEARCH

SM a SH: a benchmarking toolkit for human genome variant calling

(2014) Ameet Talwalkar et al.   BIOINFORMATICS

Tedna: a transposable element de novo assembler

(2014) Matthias Zytnicki et al.   BIOINFORMATICS

Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution

(2014) Biao Wang et al.   BMC GENOMICS

Genome sequence of Anopheles sinensis provides insight into genetics basis of mosquito competence for malaria parasites

(2014) Dan Zhou et al.   BMC GENOMICS

Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation

(2014) J. L. Wegrzyn et al.   GENETICS

Widespread contribution of transposable elements to the innovation of gene regulatory networks

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

The genome sequence of the orchid Phalaenopsis equestris

(2014) Jing Cai et al.   NATURE GENETICS

The common marmoset genome provides insight into primate biology and evolution

(2014) Kim C Worley et al.   NATURE GENETICS

Genome sequence and genetic diversity of the common carp, Cyprinus carpio

(2014) Peng Xu et al.   NATURE GENETICS

Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle

(2014) Songlin Chen et al.   NATURE GENETICS

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

(2014) Seungill Kim et al.   NATURE GENETICS

Genome sequence of the cultivated cotton Gossypium arboreum

(2014) Fuguang Li et al.   NATURE GENETICS

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

(2014) Muhua Wang et al.   NATURE GENETICS

T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data

(2014) Anna-Sophie Fiston-Lavier et al.   NUCLEIC ACIDS RESEARCH

RepARK—de novo creation of repeat libraries from whole-genome NGS reads

(2014) Philipp Koch et al.   NUCLEIC ACIDS RESEARCH

Realistic artificial DNA sequences as negative controls for computational genomics

(2014) Juan Caballero et al.   NUCLEIC ACIDS RESEARCH

Deep Investigation of Arabidopsis thaliana Junk DNA Reveals a Continuum between Repetitive Elements and Genomic Dark Matter

(2014) Florian Maumus et al.   PLoS One

Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

(2014) C. Qin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis

(2014) et al.   SCIENCE

The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle

(2014) W. Wang et al.   Nature Communications

The tobacco genome sequence and its comparison with those of tomato and potato

(2014) Nicolas Sierro et al.   Nature Communications

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

(2014) Camille Berthelot et al.   Nature Communications

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

nhmmer: DNA homology search with profile HMMs

(2013) T. J. Wheeler et al.   BIOINFORMATICS

Comparing somatic mutation-callers: beyond Venn diagrams

(2013) Su Kim et al.   BMC BIOINFORMATICS

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

(2013) Annabelle Haudry et al.   NATURE GENETICS

Transposable elements as genetic regulatory substrates in early development

(2013) Wesley D. Gifford et al.   TRENDS IN CELL BIOLOGY

Arguments for standardizing transposable element annotation in plant genomes

(2013) Raja Ragupathy et al.   TRENDS IN PLANT SCIENCE

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

RetroSeq: transposable element discovery from next-generation sequencing data

(2012) Thomas M. Keane et al.   BIOINFORMATICS

Dfam: a database of repetitive DNA based on profile hidden Markov models

(2012) Travis J. Wheeler et al.   NUCLEIC ACIDS RESEARCH

Mobile elements in the human genome: implications for disease

(2012) Szilvia Solyom et al.   Genome Medicine

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

(2012) David Kelley et al.   GENOME BIOLOGY

The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata

(2012) Nicole de la Chaux et al.   Mobile DNA

Transposable element origins of epigenetic gene regulation

(2011) Damon Lisch et al.   CURRENT OPINION IN PLANT BIOLOGY

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

(2011) Tina T Hu et al.   NATURE GENETICS

Dynamic interactions between transposable elements and their hosts

(2011) Henry L. Levin et al.   NATURE REVIEWS GENETICS

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Exploring Repetitive DNA Landscapes Using REPCLASS, a Tool That Automates the Classification of Transposable Elements in Eukaryotic Genomes

(2009) Cédric Feschotte et al.   Genome Biology and Evolution

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

(2009) E Lerat   HEREDITY

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

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

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm

(2008) Jeremy D DeBarry et al.   BMC BIOINFORMATICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

A universal classification of eukaryotic transposable elements implemented in Repbase

(2008) Vladimir V. Kapitonov et al.   NATURE REVIEWS GENETICS

The whole alignment and nothing but the alignment: the problem of spurious alignment flanks

(2008) Martin C. Frith et al.   NUCLEIC ACIDS RESEARCH

Empirical comparison of ab initio repeat finding programs

(2008) S. Saha et al.   NUCLEIC ACIDS RESEARCH

Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences

(2008) Surya Saha et al.   Tropical Plant Biology