Variation in proviral content among human genomes mediated by LTR recombination

HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini

(2018) Nicole Grandi et al.   BMC EVOLUTIONARY BIOLOGY

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis

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

Human Endogenous Retroviruses in Neurological Diseases

(2018) Patrick Küry et al.   TRENDS IN MOLECULAR MEDICINE

MYC Releases Early Reprogrammed Human Cells from Proliferation Pause via Retinoblastoma Protein Inhibition

(2018) Tim A. Rand et al.   Cell Reports

Human Endogenous Retroviruses and Their Putative Role in the Development of Autoimmune Disorders Such as Multiple Sclerosis

(2018) Victoria Gröger et al.   Frontiers in Microbiology

HERVs New Role in Cancer: From Accused Perpetrators to Cheerful Protectors

(2018) Norbert Bannert et al.   Frontiers in Microbiology

HERV Envelope Proteins: Physiological Role and Pathogenic Potential in Cancer and Autoimmunity

(2018) Nicole Grandi et al.   Frontiers in Microbiology

Human transposable elements in Repbase: genomic footprints from fish to humans

(2018) Kenji K. Kojima   Mobile DNA

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

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

HEMO, an ancestral endogenous retroviral envelope protein shed in the blood of pregnant women and expressed in pluripotent stem cells and tumors

(2017) Odile Heidmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Type W Human Endogenous Retrovirus (HERV-W) Integrations and Their Mobilization by L1 Machinery: Contribution to the Human Transcriptome and Impact on the Host Physiopathology

(2017) Nicole Grandi et al.   Viruses-Basel

Co-option of endogenous viral sequences for host cell function

(2017) John A .Frank et al.   Current Opinion in Virology

Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors

(2017) Daniel Blanco-Melo et al.   eLife

Using bioinformatic and phylogenetic approaches to classify transposable elements and understand their complex evolutionary histories

(2017) Irina R. Arkhipova   Mobile DNA

Detection of an Immunogenic HERV-E Envelope with Selective Expression in Clear Cell Kidney Cancer

(2016) Elena Cherkasova et al.   CANCER RESEARCH

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

(2016) Swapan Mallick et al.   NATURE

Regulatory activities of transposable elements: from conflicts to benefits

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

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

Contribution of type W human endogenous retroviruses to the human genome: characterization of HERV-W proviral insertions and processed pseudogenes

(2016) Nicole Grandi et al.   Retrovirology

Classification and characterization of human endogenous retroviruses; mosaic forms are common

(2016) Laura Vargiu et al.   Retrovirology

Evidence of extensive non-allelic gene conversion among LTR elements in the human genome

(2016) Beniamino Trombetta et al.   Scientific Reports

Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved

(2016) Patrick Gemmell et al.   PLoS Computational Biology

Human Endogenous Retroviruses as Pathogenic Factors in the Development of Schizophrenia

(2016) Gorjan Slokar et al.   Frontiers in Psychiatry

Human endogenous retroviruses and cancer

(2016) Gonzalez-Cao María et al.   Cancer Biology & Medicine

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

Pluripotency and the endogenous retrovirus HERVH: Conflict or serendipity?

(2015) Zsuzsanna Izsvák et al.   BIOESSAYS

Fighting Fire with Fire: Endogenous Retrovirus Envelopes as Restriction Factors

(2015) Ray Malfavon-Borja et al.   JOURNAL OF VIROLOGY

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

(2015) Edward J. Grow et al.   NATURE

The Dfam database of repetitive DNA families

(2015) Robert Hubley et al.   NUCLEIC ACIDS RESEARCH

Human endogenous retrovirus HERV-K(HML-2) activity in prostate cancer is dominated by a few loci

(2015) Wolfgang Goering et al.   PROSTATE

Genome-wide amplification of proviral sequences reveals new polymorphic HERV-K(HML-2) proviruses in humans and chimpanzees that are absent from genome assemblies

(2015) Catriona M Macfarlane et al.   Retrovirology

Human endogenous retrovirus-K contributes to motor neuron disease

(2015) Wenxue Li et al.   Science Translational Medicine

A call for benchmarking transposable element annotation methods

(2015) Douglas R. Hoen et al.   Mobile DNA

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Unfixed Endogenous Retroviral Insertions in the Human Population

(2014) E. Marchi et al.   JOURNAL OF VIROLOGY

Novel Denisovan and Neanderthal Retroviruses

(2014) A. Lee et al.   JOURNAL OF VIROLOGY

Viruses as potential pathogenic agents in systemic lupus erythematosus

(2014) P Nelson et al.   LUPUS

Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells

(2014) Jichang Wang et al.   NATURE

The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity

(2014) Xinyi Lu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Implication of Human Endogenous Retrovirus Envelope Proteins in Placental Functions

(2014) Adjimon Lokossou et al.   Viruses-Basel

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

(2014) Marc Bailly-Bechet et al.   Mobile DNA

Identification, expression and subcellular localization of ESRG

(2013) Guifei Li et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses

(2013) R. Contreras-Galindo et al.   GENOME RESEARCH

Genome-Wide Characterization of Endogenous Retroviruses in the Bat Myotis lucifugus Reveals Recent and Diverse Infections

(2013) X. Zhuo et al.   JOURNAL OF VIROLOGY

The Database of Genomic Variants: a curated collection of structural variation in the human genome

(2013) Jeffrey R. MacDonald et al.   NUCLEIC ACIDS RESEARCH

Human-Specific HERV-K Insertion Causes Genomic Variations in the Human Genome

(2013) Wonseok Shin et al.   PLoS One

Human Endogenous Retrovirus Protein Activates Innate Immunity and Promotes Experimental Allergic Encephalomyelitis in Mice

(2013) Hervé Perron et al.   PLoS One

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes

(2012) Rita Rebollo et al.   Annual Review of Genetics

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

RetroSeq: transposable element discovery from next-generation sequencing data

(2012) Thomas M. Keane et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Human Endogenous Retrovirus K Gag Coassembles with HIV-1 Gag and Reduces the Release Efficiency and Infectivity of HIV-1

(2012) K. Monde et al.   JOURNAL OF VIROLOGY

How important are transposons for plant evolution?

(2012) Damon Lisch   NATURE REVIEWS GENETICS

The endogenous retroviral envelope protein syncytin-1 inhibits LPS/PHA-stimulated cytokine responses in human blood and is sorted into placental exosomes

(2012) J.M. Tolosa et al.   PLACENTA

Retrotransposons Control Fruit-Specific, Cold-Dependent Accumulation of Anthocyanins in Blood Oranges

(2012) E. Butelli et al.   PLANT CELL

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency

(2012) Federico A Santoni et al.   Retrovirology

Landscape of Somatic Retrotransposition in Human Cancers

(2012) E. Lee et al.   SCIENCE

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

(2012) Christoffer Nellåker et al.   GENOME BIOLOGY

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

(2012) David Kelley et al.   GENOME BIOLOGY

Human Endogenous Retrovirus K106 (HERV-K106) Was Infectious after the Emergence of Anatomically Modern Humans

(2011) Aashish R. Jha et al.   PLoS One

Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses

(2011) Ravi P Subramanian et al.   Retrovirology

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A role for human endogenous retrovirus-K (HML-2) in rheumatoid arthritis: investigating mechanisms of pathogenesis

(2010) G. Freimanis et al.   CLINICAL AND EXPERIMENTAL IMMUNOLOGY

The enemy within: dormant retroviruses awaken

(2010) Michael E Engel et al.   NATURE MEDICINE

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

On the Estimation of the Insertion Time of LTR Retrotransposable Elements

(2009) T.E. Kijima et al.   MOLECULAR BIOLOGY AND EVOLUTION

Effects of Retroviruses on Host Genome Function

(2008) Patric Jern et al.   Annual Review of Genetics

Mapping and sequencing of structural variation from eight human genomes

(2008) Jeffrey M. Kidd et al.   NATURE

IDT SciTools: a suite for analysis and design of nucleic acid oligomers

(2008) R. Owczarzy et al.   NUCLEIC ACIDS RESEARCH