TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data

ERVcaller: Identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data

(2019) Xun Chen et al.   BIOINFORMATICS

LINE-1 Evasion of Epigenetic Repression in Humans

(2019) Francisco J. Sanchez-Luque et al.   MOLECULAR CELL

AluMine: alignment-free method for the discovery of polymorphic Alu element insertions

(2019) Tarmo Puurand et al.   Mobile DNA

Warning SINEs: Alu elements, evolution of the human brain, and the spectrum of neurological disease

(2018) Peter A. Larsen et al.   CHROMOSOME RESEARCH

Evidence for positive selection on recent human transposable element insertions

(2018) Lavanya Rishishwar et al.   GENE

ALUminating the Path of Atherosclerosis Progression: Chaos Theory Suggests a Role for Alu Repeats in the Development of Atherosclerotic Vascular Disease

(2018) Miguel Hueso et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms

(2018) Vallmer E. Jordan et al.   Mobile DNA

Computational tools to unmask transposable elements

(2018) Patricia Goerner-Potvin et al.   NATURE REVIEWS GENETICS

To ERV Is Human: A Phenotype-Wide Scan Linking Polymorphic Human Endogenous Retrovirus-K Insertions to Complex Phenotypes

(2018) Amelia D. Wallace et al.   Frontiers in Genetics

High-resolution genetic mapping of putative causal interactions between regions of open chromatin

(2018) Natsuhiko Kumasaka et al.   NATURE GENETICS

Alu insertion variants alter mRNA splicing

(2018) Lindsay M Payer et al.   NUCLEIC ACIDS RESEARCH

True Homoplasy of Retrotransposon Insertions in Primates

(2018) Liliya Doronina et al.   SYSTEMATIC BIOLOGY

Variation in proviral content among human genomes mediated by LTR recombination

(2018) Jainy Thomas et al.   Mobile DNA

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

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

Structural variants caused byAluinsertions are associated with risks for many human diseases

(2017) Lindsay M. Payer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Revisiting the Relationship between Transposable Elements and the Eukaryotic Stress Response

(2017) Vivien Horváth et al.   TRENDS IN GENETICS

Transposable Element Domestication As an Adaptation to Evolutionary Conflicts

(2017) Diwash Jangam et al.   TRENDS IN GENETICS

Human Retrotransposon Insertion Polymorphisms Are Associated with Health and Disease via Gene Regulatory Phenotypes

(2017) Lu Wang et al.   Frontiers in Microbiology

RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing

(2017) Jinfeng Chen et al.   PeerJ

Modelingcis-regulation with a compendium of genome-wide histone H3K27ac profiles

(2016) Su Wang et al.   GENOME RESEARCH

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

(2016) Swapan Mallick et al.   NATURE

Regulatory activities of transposable elements: from conflicts to benefits

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

Roles for retrotransposon insertions in human disease

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

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

(2015) Natsuhiko Kumasaka et al.   NATURE GENETICS

Transposable element polymorphisms recapitulate human evolution

(2015) Lavanya Rishishwar et al.   Mobile DNA

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

Space-efficient and exact de Bruijn graph representation based on a Bloom filter

(2013) Rayan Chikhi et al.   Algorithms for Molecular Biology

Transposable Elements: Powerful Contributors to Angiosperm Evolution and Diversity

(2013) Keith R. Oliver et al.   Genome Biology and Evolution

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

RetroSeq: transposable element discovery from next-generation sequencing data

(2012) Thomas M. Keane et al.   BIOINFORMATICS

Active human retrotransposons: variation and disease

(2012) Dustin C Hancks et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Landscape of Somatic Retrotransposition in Human Cancers

(2012) E. Lee et al.   SCIENCE

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Families of transposable elements, population structure and the origin of species

(2011) Jerzy Jurka et al.   Biology Direct

A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues

(2011) Athma A. Pai et al.   PLoS Genetics

A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans

(2011) Chip Stewart et al.   PLoS Genetics

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) J. Xing et al.   GENOME RESEARCH