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

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

(2016) Jennifer A Erwin et al.   NATURE NEUROSCIENCE

Resolving rates of mutation in the brain using single-neuron genomics

(2016) Gilad D Evrony et al.   eLife

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

Ubiquitous L1 Mosaicism in Hippocampal Neurons

(2015) Kyle R. Upton et al.   CELL

Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution

(2015) Adam D. Ewing et al.   GENOME RESEARCH

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

(2015) Peter H. Sudmant et al.   NATURE

Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma

(2015) Nemanja Rodić et al.   NATURE MEDICINE

LINE-1 expression and retrotransposition in Barrett’s esophagus and esophageal carcinoma

(2015) Tara T. Doucet-O'Hare et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long Interspersed Element-1 Protein Expression Is a Hallmark of Many Human Cancers

(2014) Nemanja Rodić et al.   AMERICAN JOURNAL OF PATHOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) E. Helman et al.   GENOME RESEARCH

euL1db: the European database of L1HS retrotransposon insertions in humans

(2014) Ashfaq A. Mir et al.   NUCLEIC ACIDS RESEARCH

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

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

Endogenous Retrotransposition Activates Oncogenic Pathways in Hepatocellular Carcinoma

(2013) Ruchi Shukla et al.   CELL

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

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

Combining multiple ChIP-seq peak detection systems using combinatorial fusion

(2012) Christina Schweikert et al.   BMC GENOMICS

Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain

(2012) Gilad D. Evrony et al.   CELL

Human Transposon Tectonics

(2012) Kathleen H. Burns et al.   CELL

Extensive somatic L1 retrotransposition in colorectal tumors

(2012) S. Solyom et al.   GENOME RESEARCH

Landscape of Somatic Retrotransposition in Human Cancers

(2012) E. Lee et al.   SCIENCE

Retrotransposition of marked SVA elements by human L1s in cultured cells

(2011) Dustin C. Hancks et al.   HUMAN MOLECULAR GENETICS

A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans

(2011) Chip Stewart et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) David J Witherspoon et al.   BMC GENOMICS

Mobile Interspersed Repeats Are Major Structural Variants in the Human Genome

(2010) Cheng Ran Lisa Huang et al.   CELL

Natural Mutagenesis of Human Genomes by Endogenous Retrotransposons

(2010) Rebecca C. Iskow et al.   CELL

Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans

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

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

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY