Unraveling the features of somatic transposition in the Drosophila intestine

Our Conflict with Transposable Elements and Its Implications for Human Disease

(2020) Kathleen H. Burns   Annual Review of Pathology-Mechanisms of Disease

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

(2020) Bernardo Rodriguez-Martin et al.   NATURE GENETICS

A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore

(2020) Mourdas Mohamed et al.   Cells

Transposon expression in the Drosophila brain is driven by neighboring genes and diversifies the neural transcriptome

(2020) Christoph D. Treiber et al.   GENOME RESEARCH

Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling

(2020) Adam D. Ewing et al.   MOLECULAR CELL

Author Correction: Regulation of transposable elements by DNA modifications

(2019) Özgen Deniz et al.   NATURE REVIEWS GENETICS

Stem Cell Proliferation Is Kept in Check by the Chromatin Regulators Kismet/CHD7/CHD8 and Trr/MLL3/4

(2019) Louis Gervais et al.   DEVELOPMENTAL CELL

The Landscape of L1 Retrotransposons in the Human Genome Is Shaped by Pre-insertion Sequence Biases and Post-insertion Selection

(2019) Tania Sultana et al.   MOLECULAR CELL

Cellular labeling of endogenous retrovirus replication (CLEVR) reveals de novo insertions of the gypsy retrotransposable element in cell culture and in both neurons and glial cells of aging fruit flies

(2019) Yung-Heng Chang et al.   PLOS BIOLOGY

LINE-1 Evasion of Epigenetic Repression in Humans

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

Host–transposon interactions: conflict, cooperation, and cooption

(2019) Rachel L Cosby et al.   GENES & DEVELOPMENT

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Transcriptome analyses of tumor-adjacent somatic tissues reveal genes co-expressed with transposable elements

(2019) Nicky Chung et al.   Mobile DNA

Exploratory analysis of transposable elements expression in the C. elegans early embryo

(2019) Federico Ansaloni et al.   BMC BIOINFORMATICS

The epigenomic landscape of transposable elements across normal human development and anatomy

(2019) Erica C. Pehrsson et al.   Nature Communications

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

The Retrotransposon storm and the dangers of a Collyer's genome

(2018) Josh Dubnau   CURRENT OPINION IN GENETICS & DEVELOPMENT

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis

(2018) Stephanie N. Schauer et al.   GENOME RESEARCH

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Integration site selection by retroviruses and transposable elements in eukaryotes

(2017) Tania Sultana et al.   NATURE REVIEWS GENETICS

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

L1 Mosaicism in Mammals: Extent, Effects, and Evolution

(2017) Geoffrey J. Faulkner et al.   TRENDS IN GENETICS

Chromatin state changes during neural development revealed by in vivo cell-type specific profiling

(2017) Owen J. Marshall et al.   Nature Communications

Piwi Is Required to Limit Exhaustion of Aging Somatic Stem Cells

(2017) Pedro Sousa-Victor et al.   Cell Reports

Resolving the prevalence of somatic transposition in Drosophila

(2017) Christoph D Treiber et al.   eLife

Atropos: specific, sensitive, and speedy trimming of sequencing reads

(2017) John P. Didion et al.   PeerJ

Hide and seek: how chromatin-based pathways silence retroelements in the mammalian germline

(2016) Antoine Molaro et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Somatic recombination in adult tissues: What is there to learn?

(2016) Katarzyna Siudeja et al.   FLY

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

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

Engineered LINE-1 retrotransposition in nondividing human neurons

(2016) Angela Macia et al.   GENOME RESEARCH

Somatically Acquired LINE-1 Insertions in Normal Esophagus Undergo Clonal Expansion in Esophageal Squamous Cell Carcinoma

(2016) Tara T. Doucet-O'Hare et al.   HUMAN MUTATION

Genome-wide Profiling Reveals Remarkable Parallels Between Insertion Site Selection Properties of the MLV Retrovirus and the piggyBac Transposon in Primary Human CD4+ T Cells

(2016) Andreas Gogol-Döring et al.   MOLECULAR THERAPY

The industrial melanism mutation in British peppered moths is a transposable element

(2016) Arjen E. van’t Hof et al.   NATURE

Natural courtship song variation caused by an intronic retroelement in an ion channel gene

(2016) Yun Ding et al.   NATURE

Regulatory activities of transposable elements: from conflicts to benefits

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

A comprehensive approach to expression of L1 loci

(2016) Prescott Deininger et al.   NUCLEIC ACIDS RESEARCH

Chromatin-modifying genetic interventions suppress age-associated transposable element activation and extend life span inDrosophila

(2016) Jason G. Wood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A somatic piRNA pathway in the Drosophila fat body ensures metabolic homeostasis and normal lifespan

(2016) Brian C. Jones et al.   Nature Communications

Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci

(2016) Claude Philippe et al.   eLife

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

(2016) Gilad D Evrony et al.   eLife

Mobile element insertions are frequent in oesophageal adenocarcinomas and can mislead paired-end sequencing analysis

(2015) Anna L. Paterson et al.   BMC GENOMICS

Ubiquitous L1 Mosaicism in Hippocampal Neurons

(2015) Kyle R. Upton et al.   CELL

Frequent Somatic Mutation in Adult Intestinal Stem Cells Drives Neoplasia and Genetic Mosaicism during Aging

(2015) Katarzyna Siudeja et al.   Cell Stem Cell

Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution

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

Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm

(2015) Meilina Ong-Abdullah et al.   NATURE

Niche appropriation by Drosophila intestinal stem cell tumours

(2015) Parthive H. Patel et al.   NATURE CELL BIOLOGY

Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma

(2015) Nemanja Rodić et al.   NATURE MEDICINE

Cell Lineage Analysis in Human Brain Using Endogenous Retroelements

(2015) Gilad D. Evrony et al.   NEURON

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

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

(2014) E. Helman et al.   GENOME RESEARCH

Mobile DNA elements in the generation of diversity and complexity in the brain

(2014) Jennifer A. Erwin et al.   NATURE REVIEWS NEUROSCIENCE

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

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

Integration of UPRER and Oxidative Stress Signaling in the Control of Intestinal Stem Cell Proliferation

(2014) Lifen Wang et al.   PLoS Genetics

A Transposable Element Insertion Confers Xenobiotic Resistance in Drosophila

(2014) Lidia Mateo et al.   PLoS Genetics

Endogenous Retrotransposition Activates Oncogenic Pathways in Hepatocellular Carcinoma

(2013) Ruchi Shukla et al.   CELL

Activation of transposable elements during aging and neuronal decline in Drosophila

(2013) Wanhe Li et al.   NATURE NEUROSCIENCE

Transposition-Driven Genomic Heterogeneity in the Drosophila Brain

(2013) P. N. Perrat et al.   SCIENCE

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

(2012) Gilad D. Evrony et al.   CELL

Extensive somatic L1 retrotransposition in colorectal tumors

(2012) S. Solyom et al.   GENOME RESEARCH

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

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

Landscape of Somatic Retrotransposition in Human Cancers

(2012) E. Lee et al.   SCIENCE

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

Somatic retrotransposition alters the genetic landscape of the human brain

(2011) J. Kenneth Baillie et al.   NATURE

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

Widespread establishment and regulatory impact of Alu exons in human genes

(2011) S. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Natural Mutagenesis of Human Genomes by Endogenous Retrotransposons

(2010) Rebecca C. Iskow et al.   CELL

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin

(2010) N. C. Riddle et al.   GENOME RESEARCH

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

L1 retrotransposition in human neural progenitor cells

(2009) Nicole G. Coufal et al.   NATURE

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Endogenous RNA Interference Provides a Somatic Defense against Drosophila Transposons

(2008) Wei-Jen Chung et al.   CURRENT BIOLOGY

An endogenous small interfering RNA pathway in Drosophila

(2008) Benjamin Czech et al.   NATURE

piRNA-mediated nuclear accumulation of retrotransposon transcripts in the Drosophila female germline

(2008) S. Chambeyron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Epigenetic Role for Maternally Inherited piRNAs in Transposon Silencing

(2008) J. Brennecke et al.   SCIENCE

Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells

(2008) M. Ghildiyal et al.   SCIENCE