Pedigree-based estimation of human mobile element retrotransposition rates

Multi-platform discovery of haplotype-resolved structural variation in human genomes

(2019) Mark J. P. Chaisson et al.   Nature Communications

Heritable L1 Retrotransposition Events During Development: Understanding Their Origins

(2018) Sandra R. Richardson et al.   BIOESSAYS

An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder

(2018) Donna M. Werling et al.   NATURE GENETICS

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

L1 retrotransposition in the soma: a field jumping ahead

(2018) Geoffrey J. Faulkner et al.   Mobile DNA

Computational tools to unmask transposable elements

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

Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy

(2018) Betsy E. P. Ostrander et al.   npj Genomic Medicine

Multiple transmissions of de novo mutations in families

(2018) Hákon Jónsson et al.   NATURE GENETICS

Heritable L1 retrotransposition in the mouse primordial germline and early embryo

(2017) Sandra R. Richardson et al.   GENOME RESEARCH

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

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

Parental influence on human germline de novo mutations in 1,548 trios from Iceland

(2017) Hákon Jónsson et al.   NATURE

Genome-wide profiling of heritable and de novo STR variations

(2017) Thomas Willems et al.   NATURE METHODS

Mobile DNA in Health and Disease

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

Intact piRNA pathway prevents L1 mobilization in male meiosis

(2017) Simon J. Newkirk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of rare, diagnostic AluYb8/9 elements in diverse human populations

(2017) Julie Feusier et al.   Mobile DNA

Insertion and deletion polymorphisms of the ancient AluS family in the human genome

(2017) Maria S. Kryatova et al.   Mobile DNA

Benchmarking computational tools for polymorphic transposable element detection

(2016) Lavanya Rishishwar et al.   BRIEFINGS IN BIOINFORMATICS

A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer

(2016) Emma C. Scott et al.   GENOME RESEARCH

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

(2016) Swapan Mallick et al.   NATURE

L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes

(2016) Tobias Penzkofer et al.   NUCLEIC ACIDS RESEARCH

Discovery of unfixed endogenous retrovirus insertions in diverse human populations

(2016) Julia Halo Wildschutte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Retrotransposons as regulators of gene expression

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

Restricting retrotransposons: a review

(2016) John L. Goodier   Mobile DNA

Roles for retrotransposon insertions in human disease

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

Post-zygotic Point Mutations Are an Underrecognized Source of De Novo Genomic Variation

(2015) Rocio Acuna-Hidalgo et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Sequence Analysis and Characterization of Active HumanAlusubfamilies Based on the 1000 Genomes Pilot Project

(2015) Miriam K. Konkel et al.   Genome Biology and Evolution

Timing, rates and spectra of human germline mutation

(2015) Raheleh Rahbari et al.   NATURE GENETICS

Efficient genotype compression and analysis of large genetic-variation data sets

(2015) Ryan M Layer et al.   NATURE METHODS

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Transposable element detection from whole genome sequence data

(2015) Adam D. Ewing   Mobile DNA

Parental Somatic Mosaicism Is Underrecognized and Influences Recurrence Risk of Genomic Disorders

(2014) Ian M. Campbell et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Determinants of Mutation Rate Variation in the Human Germline

(2014) Laure Ségurel et al.   Annual Review of Genomics and Human Genetics

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

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

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

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division

(2013) A. Abyzov et al.   GENOME RESEARCH

Properties and rates of germline mutations in humans

(2013) Catarina D. Campbell et al.   TRENDS IN GENETICS

Gene Copy-Number Polymorphism Caused by Retrotransposition in Humans

(2013) Daniel R. Schrider et al.   PLoS Genetics

Retrotransposition of gene transcripts leads to structural variation in mammalian genomes

(2013) Adam D Ewing et al.   GENOME BIOLOGY

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

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

Active human retrotransposons: variation and disease

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

Consanguinity in Centre d’Étude du Polymorphisme Humain (CEPH) pedigrees

(2012) Eric L Stevens et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

The genomic landscape shaped by selection on transposable elements across 18 mouse strains

(2012) Christoffer Nellåker et al.   GENOME BIOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Novel family of human transposable elements formed due to fusion of the first exon of gene MAST2 with retrotransposon SVA

(2010) O. B. Bantysh et al.   BIOCHEMISTRY-MOSCOW

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Mobile Interspersed Repeats Are Major Structural Variants in the Human Genome

(2010) Cheng Ran Lisa Huang 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

Alu repeat discovery and characterization within human genomes

(2010) F. Hormozdiari et al.   GENOME RESEARCH

Fine-scale recombination rate differences between sexes, populations and individuals

(2010) Augustine Kong et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

PRDM9 Is a Major Determinant of Meiotic Recombination Hotspots in Humans and Mice

(2010) F. Baudat et al.   SCIENCE

Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing

(2010) J. C. Roach et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism

(2009) H. Kano et al.   GENES & DEVELOPMENT

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

(2009) J. Xing et al.   GENOME RESEARCH

Exon-trapping mediated by the human retrotransposon SVA

(2009) D. C. Hancks et al.   GENOME RESEARCH

5'-Transducing SVA retrotransposon groups spread efficiently throughout the human genome

(2009) A. Damert et al.   GENOME RESEARCH

Fine-scaled human genetic structure revealed by SNP microarrays

(2009) J. Xing et al.   GENOME RESEARCH

Diverse cis factors controlling Alu retrotransposition: What causes Alu elements to die?

(2009) M. S. Comeaux et al.   GENOME RESEARCH

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

From Linkage Maps to Quantitative Trait Loci: The History and Science of the Utah Genetic Reference Project

(2008) Stephen M. Prescott et al.   Annual Review of Genomics and Human Genetics

Active Alu retrotransposons in the human genome

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