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

Primer3_masker: integrating masking of template sequence with primer design software

(2018) Triinu Kõressaar et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   DNA RESEARCH

Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel

(2017) Mario Mitt et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Mobile DNA in Health and Disease

(2017) Haig H. Kazazian et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

ALU ternative Regulation for Gene Expression

(2017) Ling-Ling Chen et al.   TRENDS IN CELL BIOLOGY

FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads

(2017) Fanny-Dhelia Pajuste et al.   Scientific Reports

Population-wide sampling of retrotransposon insertion polymorphisms using deep sequencing and efficient detection

(2017) Qichao Yu et al.   GigaScience

Retrotransposons as regulators of gene expression

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

Identification of human-specific AluS elements through comparative genomics

(2015) Jae Lee et al.   GENE

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

(2015) Peter H. Sudmant et al.   NATURE

The Dfam database of repetitive DNA families

(2015) Robert Hubley et al.   NUCLEIC ACIDS RESEARCH

Tangram: a comprehensive toolbox for mobile element insertion detection

(2014) Jiantao Wu et al.   BMC GENOMICS

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

Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations

(2013) D. J. Witherspoon et al.   GENOME RESEARCH

Detecting Alu insertions from high-throughput sequencing data

(2013) Matei David et al.   NUCLEIC ACIDS RESEARCH

RetroSeq: transposable element discovery from next-generation sequencing data

(2012) Thomas M. Keane et al.   BIOINFORMATICS

SINE Retrotransposons Cause Epigenetic Reprogramming of Adjacent Gene Promoters

(2012) M. R. H. Estecio et al.   MOLECULAR CANCER RESEARCH

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

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

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

Mobile elements in the human genome: implications for disease

(2012) Szilvia Solyom et al.   Genome Medicine

Novel polymorphic AluYb8 insertion in the WNK1 gene is associated with blood pressure variation in Europeans

(2011) Margus Putku et al.   HUMAN MUTATION

A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans

(2011) Chip Stewart et al.   PLoS Genetics

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

(2010) Fereydoun Hormozdiari et al.   BIOINFORMATICS

Alu repeat discovery and characterization within human genomes

(2010) F. Hormozdiari et al.   GENOME RESEARCH

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

(2010) A. R. Quinlan et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) J. Xing et al.   GENOME RESEARCH

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

(2008) Tim Hulsen et al.   BMC GENOMICS

Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health

(2008) V. P. Belancio et al.   GENOME RESEARCH

Active Alu retrotransposons in the human genome

(2008) E. A. Bennett et al.   GENOME RESEARCH