Organ-, sex- and age-dependent patterns of endogenous L1 mRNA expression at a single locus resolution

Comparative analysis on the expression of L1 loci using various RNA-Seq preparations

(2020) Tiffany Kaul et al.   Mobile DNA

Vertebrate Lineages Exhibit Diverse Patterns of Transposable Element Regulation and Expression across Tissues

(2020) Giulia I M Pasquesi et al.   Genome Biology and Evolution

Mouse germ line mutations due to retrotransposon insertions

(2019) Liane Gagnier et al.   Mobile DNA

L1EM: a tool for accurate locus specific LINE-1 RNA quantification

(2019) Wilson McKerrow et al.   BIOINFORMATICS

Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival

(2019) Tatiana Cajuso et al.   Nature Communications

Transcriptional Signatures of Aging

(2017) R. Stegeman et al.   JOURNAL OF MOLECULAR BIOLOGY

Mechanisms of HERV-K (HML-2) Transcription during Human Mammary Epithelial Cell Transformation

(2017) Meagan Montesion et al.   JOURNAL OF VIROLOGY

Differential analysis of RNA-seq incorporating quantification uncertainty

(2017) Harold Pimentel et al.   NATURE METHODS

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

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

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

Modeling menopause: The utility of rodents in translational behavioral endocrinology research

(2016) Stephanie V. Koebele et al.   MATURITAS

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

A comprehensive approach to expression of L1 loci

(2016) Prescott Deininger et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Tobias Penzkofer et al.   NUCLEIC ACIDS RESEARCH

Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells

(2016) Sabine Klawitter 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

Restricting retrotransposons: a review

(2016) John L. Goodier   Mobile DNA

Transposable elements become active and mobile in the genomes of aging mammalian somatic tissues

(2016) Marco De Cecco et al.   Aging-US

TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets

(2015) Ying Jin et al.   BIOINFORMATICS

miR-128 represses L1 retrotransposition by binding directly to L1 RNA

(2015) Matthias Hamdorf et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

miR-128 represses L1 retrotransposition by binding directly to L1 RNA

(2015) Matthias Hamdorf et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Contribution of Alu Elements to Mutagenic DNA Double-Strand Break Repair

(2015) Maria E. Morales et al.   PLoS Genetics

The Broad-Spectrum Antiviral Protein ZAP Restricts Human Retrotransposition

(2015) John L. Goodier et al.   PLoS Genetics

The aging clock and circadian control of metabolism and genome stability

(2015) Victoria P. Belancio et al.   Frontiers in Genetics

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

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

Transcriptional landscape of repetitive elements in normal and cancer human cells

(2014) Steven W Criscione et al.   BMC GENOMICS

Potential for genomic instability associated with retrotranspositionally-incompetent L1 loci

(2014) Kristine J. Kines et al.   NUCLEIC ACIDS RESEARCH

Regulation of L1 expression and retrotransposition by melatonin and its receptor: implications for cancer risk associated with light exposure at night

(2014) Dawn deHaro et al.   NUCLEIC ACIDS RESEARCH

Sleeping dogs of the genome

(2014) Vera Gorbunova et al.   SCIENCE

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

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

SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age

(2014) Michael Van Meter et al.   Nature Communications

Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements

(2013) Marco De Cecco et al.   AGING CELL

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

(2013) Ning Leng et al.   BIOINFORMATICS

Changes in Mouse Uterine Transcriptome in Estrus and Proestrus1

(2013) Kerri Stanley Yip et al.   BIOLOGY OF REPRODUCTION

Revisiting the evolution of mouse LINE-1 in the genomic era

(2013) Akash Sookdeo et al.   Mobile DNA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

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

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

Landscape of Somatic Retrotransposition in Human Cancers

(2012) E. Lee et al.   SCIENCE

LINE-1 Elements in Structural Variation and Disease

(2011) Christine R. Beck et al.   Annual Review of Genomics and Human Genetics

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

LINE-1 Retrotransposition Activity in Human Genomes

(2010) Christine R. Beck et al.   CELL

A LINE-1 component to human aging: Do LINE elements exact a longevity cost for evolutionary advantage?

(2010) Georges St. Laurent et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Somatic expression of LINE-1 elements in human tissues

(2010) Victoria P. Belancio et al.   NUCLEIC ACIDS RESEARCH

All y’all need to know ‘bout retroelements in cancer

(2010) Victoria P. Belancio et al.   SEMINARS IN CANCER BIOLOGY

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

(2009) J. Xing et al.   GENOME RESEARCH

Epigenetic control of mammalian LINE-1 retrotransposon by retinoblastoma proteins

(2009) Diego E. Montoya-Durango et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

ERCC1/XPF limits L1 retrotransposition

(2008) Stephen L. Gasior et al.   DNA REPAIR

The impact of multiple splice sites in human L1 elements

(2008) V.P. Belancio et al.   GENE

L1 mobile element expression causes multiple types of toxicity

(2008) Nicholas A. Wallace et al.   GENE

Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition

(2008) K. Akagi et al.   GENOME RESEARCH