Computational tools to unmask transposable elements

SimulaTE: simulating complex landscapes of transposable elements of populations

(2018) Robert Kofler   BIOINFORMATICS

A high throughput screen for active human transposable elements

(2018) Erika M. Kvikstad et al.   BMC GENOMICS

Identifying co-opted transposable elements using comparative epigenomics

(2018) David Venuto et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

FishTEDB: a collective database of transposable elements identified in the complete genomes of fish

(2018) Feng Shao et al.   Database-The Journal of Biological Databases and Curation

Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells

(2018) Yoav Lubelsky et al.   NATURE

The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology

(2017) Eugene J. Gardner et al.   GENOME RESEARCH

Evaluation and assessment of read-mapping by multiple next-generation sequencing aligners based on genome-wide characteristics

(2017) Subazini Thankaswamy-Kosalai et al.   GENOMICS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer

(2017) Zuojian Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data

(2017) Michael G. Nelson et al.   G3-Genes Genomes Genetics

Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants

(2017) Sophie Lanciano et al.   PLoS Genetics

LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences

(2017) Eric Disdero et al.   Mobile DNA

phRAIDER: Pattern-Hunter based Rapid Ab Initio Detection of Elementary Repeats

(2016) Carly E. Schaeffer et al.   BIOINFORMATICS

MGEScan: a Galaxy-based system for identifying retrotransposons in genomes

(2016) Hyungro Lee et al.   BIOINFORMATICS

Next-generation sequencing-based detection of germline L1-mediated transductions

(2016) Jelena Tica et al.   BMC GENOMICS

Not so bad after all: retroviruses and long terminal repeat retrotransposons as a source of new genes in vertebrates

(2016) M. Naville et al.   CLINICAL MICROBIOLOGY AND INFECTION

Discovery and genotyping of structural variation from long-read haploid genome sequence data

(2016) John Huddleston et al.   GENOME RESEARCH

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

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

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

L1-associated genomic regions are deleted in somatic cells of the healthy human brain

(2016) Jennifer A Erwin et al.   NATURE NEUROSCIENCE

Regulatory activities of transposable elements: from conflicts to benefits

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

Repetitive sequences and epigenetic modification: inseparable partners play important roles in the evolution of plant sex chromosomes

(2016) Shu-Fen Li et al.   PLANTA

Retrotransposons as regulators of gene expression

(2016) R. A. Elbarbary et al.   SCIENCE

Regulatory evolution of innate immunity through co-option of endogenous retroviruses

(2016) E. B. Chuong et al.   SCIENCE

gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes

(2016) So Nakagawa et al.   Database-The Journal of Biological Databases and Curation

The Arabidopsis thaliana mobilome and its impact at the species level

(2016) Leandro Quadrana et al.   eLife

Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

(2016) Tim Stuart et al.   eLife

Endogenous retroviral promoter exaptation in human cancer

(2016) Artem Babaian et al.   Mobile DNA

Roles for retrotransposon insertions in human disease

(2016) Dustin C. Hancks et al.   Mobile DNA

MMR: a tool for read multi-mapper resolution

(2015) André Kahles et al.   BIOINFORMATICS

TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets

(2015) Ying Jin et al.   BIOINFORMATICS

Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale

(2015) Hani Z. Girgis   BMC BIOINFORMATICS

ITIS, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data

(2015) Chuan Jiang et al.   BMC BIOINFORMATICS

RiTE database: a resource database for genus-wide rice genomics and evolutionary biology

(2015) Dario Copetti et al.   BMC GENOMICS

Sequencing, identification and mapping of primed L1 elements (SIMPLE) reveals significant variation in full length L1 elements between individuals

(2015) Vincent A Streva et al.   BMC GENOMICS

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

(2015) Elizabeth Hénaff et al.   BMC GENOMICS

De Novo Assembly and Annotation of the Asian Tiger Mosquito (Aedes albopictus) Repeatome with dnaPipeTE from Raw Genomic Reads and Comparative Analysis with the Yellow Fever Mosquito (Aedes aegypti)

(2015) Clément Goubert et al.   Genome Biology and Evolution

A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity

(2015) Benoît Piégu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

PGSB PlantsDB: updates to the database framework for comparative plant genome research

(2015) Manuel Spannagl et al.   NUCLEIC ACIDS RESEARCH

Unique transposon landscapes are pervasive acrossDrosophila melanogastergenomes

(2015) Reazur Rahman et al.   NUCLEIC ACIDS RESEARCH

The Dfam database of repetitive DNA families

(2015) Robert Hubley et al.   NUCLEIC ACIDS RESEARCH

GREAM: A Web Server to Short-List Potentially Important Genomic Repeat Elements Based on Over-/Under-Representation in Specific Chromosomal Locations, Such as the Gene Neighborhoods, within or across 17 Mammalian Species

(2015) Darshan Shimoga Chandrashekar et al.   PLoS One

Transposable element detection from whole genome sequence data

(2015) Adam D. Ewing   Mobile DNA

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Tedna: a transposable element de novo assembler

(2014) Matthias Zytnicki et al.   BIOINFORMATICS

piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing

(2014) Bo W. Han et al.   BIOINFORMATICS

Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements

(2014) Mariko Nakagome et al.   BMC BIOINFORMATICS

TE-Tracker: systematic identification of transposition events through whole-genome resequencing

(2014) Arthur Gilly et al.   BMC BIOINFORMATICS

Tangram: a comprehensive toolbox for mobile element insertion detection

(2014) Jiantao Wu et al.   BMC GENOMICS

Transcriptional landscape of repetitive elements in normal and cancer human cells

(2014) Steven W Criscione et al.   BMC GENOMICS

Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing

(2014) E. Helman et al.   GENOME RESEARCH

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity

(2014) Xinyi Lu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

euL1db: the European database of L1HS retrotransposon insertions in humans

(2014) Ashfaq A. Mir 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

TEMP: a computational method for analyzing transposable element polymorphism in populations

(2014) Jiali Zhuang et al.   NUCLEIC ACIDS RESEARCH

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes

(2014) J. M. C. Tubio et al.   SCIENCE

Retrotransposition in tumors and brains

(2014) John L Goodier   Mobile DNA

RCPedia: a database of retrocopied genes

(2013) Fábio C. P. Navarro et al.   BIOINFORMATICS

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data

(2013) Ryuichiro Nakato et al.   GENES TO CELLS

Abundance and Distribution of Transposable Elements in Two Drosophila QTL Mapping Resources

(2013) Julie M. Cridland et al.   MOLECULAR BIOLOGY AND EVOLUTION

PIWI-interacting RNAs: from generation to transgenerational epigenetics

(2013) Maartje J. Luteijn et al.   NATURE REVIEWS GENETICS

Detecting Alu insertions from high-throughput sequencing data

(2013) Matei David et al.   NUCLEIC ACIDS RESEARCH

P-MITE: a database for plant miniature inverted-repeat transposable elements

(2013) Jiongjiong Chen et al.   NUCLEIC ACIDS RESEARCH

Correction: Temporal Expression of Pelp1 during Proliferation and Osteogenic Differentiation of Rat Bone Marrow Mesenchymal Stem Cells

(2013) Jing Wang et al.   PLoS One

Active Transposition in Genomes

(2012) Cheng Ran Lisa Huang et al.   Annual Review of Genetics

RetroSeq: transposable element discovery from next-generation sequencing data

(2012) Thomas M. Keane et al.   BIOINFORMATICS

MASiVEdb: the Sirevirus Plant Retrotransposon Database

(2012) Alexandros Bousios et al.   BMC GENOMICS

The C-value paradox, junk DNA and ENCODE

(2012) Sean R. Eddy   CURRENT BIOLOGY

Nonallelic homologous recombination between retrotransposable elements is a driver of de novo unbalanced translocations

(2012) C. Robberecht et al.   GENOME RESEARCH

Extensive somatic L1 retrotransposition in colorectal tumors

(2012) S. Solyom et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

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

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

dbVar and DGVa: public archives for genomic structural variation

(2012) Ilkka Lappalainen et al.   NUCLEIC ACIDS RESEARCH

SINEBase: a database and tool for SINE analysis

(2012) Nikita S. Vassetzky et al.   NUCLEIC ACIDS RESEARCH

Whole Genome Resequencing Reveals Natural Target Site Preferences of Transposable Elements in Drosophila melanogaster

(2012) Raquel S. Linheiro et al.   PLoS One

Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster

(2012) Robert Kofler et al.   PLoS Genetics

Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions

(2011) D. He et al.   BIOINFORMATICS

Somatic retrotransposition alters the genetic landscape of the human brain

(2011) J. Kenneth Baillie et al.   NATURE

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

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

(2011) Dongjun Chung et al.   PLoS Computational Biology

MASiVE: Mapping and Analysis of SireVirus Elements in plant genome sequences

(2010) N. Darzentas et al.   BIOINFORMATICS

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

(2010) Fereydoun Hormozdiari et al.   BIOINFORMATICS

A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags

(2010) Jianrong Wang et al.   BIOINFORMATICS

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

(2010) Petr Novák et al.   BMC BIOINFORMATICS

A novel web-based TinT application and the chronology of the Primate Alu retroposon activity

(2010) Gennady Churakov et al.   BMC EVOLUTIONARY BIOLOGY

Mobile element scanning (ME-Scan) by targeted high-throughput sequencing

(2010) David J Witherspoon et al.   BMC GENOMICS

Natural Mutagenesis of Human Genomes by Endogenous Retrotransposons

(2010) Rebecca C. Iskow et al.   CELL

High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes

(2010) A. D. Ewing et al.   GENOME RESEARCH

L1 retrotransposition in neurons is modulated by MeCP2

(2010) Alysson R. Muotri et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

(2010) C. Llorens et al.   NUCLEIC ACIDS RESEARCH

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Small RNAs as Guardians of the Genome

(2009) Colin D. Malone et al.   CELL

Mobile elements create structural variation: Analysis of a complete human genome

(2009) J. Xing et al.   GENOME RESEARCH

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

(2009) E Lerat   HEREDITY

L1 retrotransposition in human neural progenitor cells

(2009) Nicole G. Coufal et al.   NATURE

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

Transposon-induced gene activation as a mechanism generating cluster shape somatic variation in grapevine

(2009) Lucie Fernandez et al.   PLANT JOURNAL

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Human Alu RNA Is a Modular Transacting Repressor of mRNA Transcription during Heat Shock

(2008) Peter D. Mariner et al.   MOLECULAR CELL

Revised nomenclature for transposable genetic elements

(2008) Adam P. Roberts et al.   PLASMID