SARS-CoV-2 infection induces epigenetic changes in the LTR69 subfamily of endogenous retroviruses

Human Endogenous Retrovirus (HERV) Transcriptome Is Dynamically Modulated during SARS-CoV-2 Infection and Allows Discrimination of COVID-19 Clinical Stages

(2023) Nicole Grandi et al.   Microbiology Spectrum

Roles of transposable elements in the regulation of mammalian transcription

(2022) Raquel Fueyo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

High Expression of HERV-K (HML-2) Might Stimulate Interferon in COVID-19 Patients

(2022) Yaolin Guo et al.   Viruses-Basel

Human endogenous retrovirus K in the respiratory tract is associated with COVID-19 physiopathology

(2022) Jairo R. Temerozo et al.   Microbiome

Impaired activation of transposable elements in SARS‐CoV ‐2 infection

(2022) Matan Sorek et al.   EMBO REPORTS

Unveiling HERV‐K113‐ENV as SARS‐CoV‐2 severity admissible biomarker by mining transcriptome data

(2022) Perumal Arumugam Desingu et al.   JOURNAL OF MEDICAL VIROLOGY

HERV-W ENV antigenemia and correlation of increased anti-SARS-CoV-2 immunoglobulin levels with post-COVID-19 symptoms

(2022) Karen Giménez-Orenga et al.   Frontiers in Immunology

Transcription start site signal profiling improves transposable element RNA expression analysis at locus-level

(2022) Natalia Savytska et al.   Frontiers in Genetics

TOP1 inhibition therapy protects against SARS-CoV-2-induced lethal inflammation

(2021) Jessica Sook Yuin Ho et al.   CELL

Systematic functional analysis of SARS-CoV-2 proteins uncovers viral innate immune antagonists and remaining vulnerabilities

(2021) Manuel Hayn et al.   Cell Reports

Evidence of the pathogenic HERV-W envelope expression in T lymphocytes in association with the respiratory outcome of COVID-19 patients

(2021) Emanuela Balestrieri et al.   EBioMedicine

Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis

(2021) Mariana G. Ferrarini et al.   Communications Biology

Enhanced Expression of Autoantigens During SARS-CoV-2 Viral Infection

(2021) Narjes Saheb Sharif-Askari et al.   Frontiers in Immunology

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

(2021) Jaime A Castro-Mondragon et al.   NUCLEIC ACIDS RESEARCH

Antiviral immunity triggered by infection-induced host transposable elements

(2021) Benjamin G Hale   Current Opinion in Virology

SARS-CoV-2 infection mediates differential expression of human endogenous retroviruses and long interspersed nuclear elements

(2021) Jez L. Marston et al.   JCI Insight

Upregulation of Human Endogenous Retroviruses in Bronchoalveolar Lavage Fluid of COVID-19 Patients

(2021) Konstantina Kitsou et al.   Microbiology Spectrum

Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

(2020) Daniel Blanco-Melo et al.   CELL

HIV-1 infection activates endogenous retroviral promoters regulating antiviral gene expression

(2020) Smitha Srinivasachar Badarinarayan et al.   NUCLEIC ACIDS RESEARCH

SARS-CoV-2 Is Restricted by Zinc Finger Antiviral Protein despite Preadaptation to the Low-CpG Environment in Humans

(2020) Rayhane Nchioua et al.   mBio

GENCODE 2021

(2020) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

An influenza virus-triggered SUMO switch orchestrates co-opted endogenous retroviruses to stimulate host antiviral immunity

(2019) Nora Schmidt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

OUP accepted manuscript

(2018)   BIOINFORMATICS

GIGGLE: a search engine for large-scale integrated genome analysis

(2018) Ryan M Layer et al.   NATURE METHODS

LNCipedia 5: towards a reference set of human long non-coding RNAs

(2018) Pieter-Jan Volders et al.   NUCLEIC ACIDS RESEARCH

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis

(2018) Rongbin Zheng et al.   NUCLEIC ACIDS RESEARCH

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Tracking the Antibody Immunome in Type 1 Diabetes Using Protein Arrays

(2016) Xiaofang Bian et al.   JOURNAL OF PROTEOME RESEARCH

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

(2015) Ying Jin et al.   BIOINFORMATICS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

LINE-1 Retrotransposable Element DNA Accumulates in HIV-1-Infected Cells

(2013) R. B. Jones et al.   JOURNAL OF VIROLOGY

Human Cytomegalovirus (HCMV) induces Human Endogenous Retrovirus (HERV) transcription

(2013) Alice Assinger et al.   Retrovirology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Modulation of NF- B-dependent gene transcription using programmable DNA minor groove binders

(2011) J. A. Raskatov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA