Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling

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

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

Mobile genomics: tools and techniques for tackling transposons

(2020) Kathryn O'Neill et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Simons Genome Diversity Project: a global analysis of mobile element diversity

(2020) W Scott Watkins et al.   Genome Biology and Evolution

Telomere-to-telomere assembly of a complete human X chromosome

(2020) Karen H. Miga et al.   NATURE

Measuring and interpreting transposable element expression

(2020) Sophie Lanciano et al.   NATURE REVIEWS GENETICS

Using long-read sequencing to detect imprinted DNA methylation

(2019) Scott Gigante et al.   NUCLEIC ACIDS RESEARCH

Transposable elements drive widespread expression of oncogenes in human cancers

(2019) Hyo Sik Jang et al.   NATURE GENETICS

L1 drives IFN in senescent cells and promotes age-associated inflammation

(2019) Marco De Cecco et al.   NATURE

Dynamic Methylation of an L1 Transduction Family during Reprogramming and Neurodifferentiation

(2019) Carmen Salvador-Palomeque et al.   MOLECULAR AND CELLULAR BIOLOGY

LINE-1 Evasion of Epigenetic Repression in Humans

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

Activation of neuronal genes via LINE-1 elements upon global DNA demethylation in human neural progenitors

(2019) Marie E Jönsson et al.   Nature Communications

The Arms Race Between KRAB–Zinc Finger Proteins and Endogenous Retroelements and Its Impact on Mammals

(2019) Melania Bruno et al.   Annual Review of Genetics

The diverse roles of DNA methylation in mammalian development and disease

(2019) Maxim V. C. Greenberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Patient-Customized Oligonucleotide Therapy for a Rare Genetic Disease

(2019) Jinkuk Kim et al.   NEW ENGLAND JOURNAL OF MEDICINE

Human-specific tandem repeat expansion and differential gene expression during primate evolution

(2019) Arvis Sulovari et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology

(2019) Weichen Zhou et al.   NUCLEIC ACIDS RESEARCH

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

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

Parallelization of MAFFT for large-scale multiple sequence alignments

(2018) Tsukasa Nakamura et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis

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

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

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

LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation

(2018) Julie Brind’Amour et al.   Nature Communications

Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance

(2018) Anastasiya Kazachenka et al.   CELL

The discovery and importance of genomic imprinting

(2018) Anne C Ferguson-Smith et al.   eLife

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

KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks

(2017) Michaël Imbeault et al.   NATURE

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

Mobile DNA in Health and Disease

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

Disease onset in X-linked dystonia-parkinsonism correlates with expansion of a hexameric repeat within an SVA retrotransposon inTAF1

(2017) D. Cristopher Bragg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing

(2017) Barun Pradhan et al.   Scientific Reports

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

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

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

(2016) Jennifer A Erwin et al.   NATURE NEUROSCIENCE

Regulatory activities of transposable elements: from conflicts to benefits

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

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

(2016) Claude Philippe et al.   eLife

An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells

(2016) Marius Walter et al.   eLife

Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme

(2016) Patricia E. Carreira et al.   Mobile DNA

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

Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites

(2015) Fiorella C. Grandi et al.   GENOME RESEARCH

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads

(2015) Murray Patterson et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2015) Peter H. Sudmant et al.   NATURE

Cell Lineage Analysis in Human Brain Using Endogenous Retroelements

(2015) Gilad D. Evrony et al.   NEURON

Transposable element detection from whole genome sequence data

(2015) Adam D. Ewing   Mobile DNA

Evolutionally dynamic L1 regulation in embryonic stem cells

(2014) N. Castro-Diaz et al.   GENES & DEVELOPMENT

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

(2014) Frank M. J. Jacobs et al.   NATURE

Endogenous Retrotransposition Activates Oncogenic Pathways in Hepatocellular Carcinoma

(2013) Ruchi Shukla et al.   CELL

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

Tabix: fast retrieval of sequence features from generic TAB-delimited files

(2011) H. Li   BIOINFORMATICS

Retrotransposition of marked SVA elements by human L1s in cultured cells

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

Pathogenic exon-trapping by SVA retrotransposon and rescue in Fukuyama muscular dystrophy

(2011) Mariko Taniguchi-Ikeda et al.   NATURE

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

(2011) Mark A DePristo et al.   NATURE GENETICS

The non-autonomous retrotransposon SVA is trans -mobilized by the human LINE-1 protein machinery

(2011) Julija Raiz et al.   NUCLEIC ACIDS RESEARCH

A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans

(2011) Chip Stewart et al.   PLoS Genetics

LINE-1 Retrotransposition Activity in Human Genomes

(2010) Christine R. Beck 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

KAP1 controls endogenous retroviruses in embryonic stem cells

(2010) Helen M. Rowe et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism

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

Exon-trapping mediated by the human retrotransposon SVA

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