Endogenous Retrovirus Elements Are Co-Expressed with IFN Stimulation Genes in the JAK–STAT Pathway

Human IFNAR2 Mutant Generated by CRISPR/Cas9-Induced Exon Skipping Upregulates a Subset of Tonic-Like Interferon-Stimulated Genes Upon IFNβ Stimulation

(2022) Linnan Zhang et al.   JOURNAL OF INTERFERON AND CYTOKINE RESEARCH

Pharmacological activation of p53 triggers viral mimicry response thereby abolishing tumor immune evasion and promoting anti-tumor immunity

(2021) Xiaolei Zhou et al.   Cancer Discovery

Specific subfamilies of transposable elements contribute to different domains of T lymphocyte enhancers

(2020) Mengliang Ye et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of the distribution of human endogenous retroviruses K (HML-2) by PCR-based target enrichment sequencing

(2020) Bei Xue et al.   Retrovirology

Transcription profile of human endogenous retroviruses in response to dengue virus serotype 2 infection

(2020) Miao Wang et al.   VIROLOGY

FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files

(2019) Leandro Gabriel Roser et al.   BMC BIOINFORMATICS

CRISPR/Cas9-based Knockout Strategy Elucidates Components Essential for Type 1 Interferon Signaling in Human HeLa Cells

(2019) Victoria Urin et al.   JOURNAL OF MOLECULAR BIOLOGY

Switching roles for DNA and histone methylation depend on evolutionary ages of human endogenous retroviruses

(2018) Hitoshi Ohtani et al.   GENOME RESEARCH

Identification of new type I interferon-stimulated genes and investigation of their involvement in IFN-β activation

(2018) Xiaolin Zhang et al.   Protein & Cell

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

(2017) Michaël Imbeault et al.   NATURE

NF-κB and IRF1 Induce Endogenous Retrovirus K Expression via Interferon-Stimulated Response Elements in Its 5′ Long Terminal Repeat

(2016) Mamneet Manghera et al.   JOURNAL OF VIROLOGY

Regulatory evolution of innate immunity through co-option of endogenous retroviruses

(2016) E. B. Chuong et al.   SCIENCE

Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data

(2015) Kerstin Haase et al.   BMC Medical Genomics

The KRAB zinc finger protein ZFP809 is required to initiate epigenetic silencing of endogenous retroviruses

(2015) Gernot Wolf et al.   GENES & DEVELOPMENT

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

PRRs are watching you: Localization of innate sensing and signaling regulators

(2015) Jonathan Chow et al.   VIROLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

Bridging the Species Divide: Transgenic Mice Humanized for Type-I Interferon Response

(2014) Daniel Harari et al.   PLoS One

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

IFNβ-dependent increases in STAT1, STAT2, and IRF9 mediate resistance to viruses and DNA damage

(2013) HyeonJoo Cheon et al.   EMBO JOURNAL

Structural basis of a unique interferon-β signaling axis mediated via the receptor IFNAR1

(2013) Nicole A de Weerd et al.   NATURE IMMUNOLOGY

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements

(2013) Pierre-Étienne Jacques et al.   PLoS Genetics

Structural and dynamic determinants of type I interferon receptor assembly and their functional interpretation

(2012) Jacob Piehler et al.   IMMUNOLOGICAL REVIEWS

Dfam: a database of repetitive DNA based on profile hidden Markov models

(2012) Travis J. Wheeler et al.   NUCLEIC ACIDS RESEARCH

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Systematic identification of type I and type II interferon-induced antiviral factors

(2012) S.-Y. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Type I interferons directly down-regulate BCL-6 in primary and transformed germinal center B cells: Differential regulation in B cell lines derived from endemic or sporadic Burkitt’s lymphoma

(2011) Daniel Salamon et al.   CYTOKINE

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

MER41 Repeat Sequences Contain Inducible STAT1 Binding Sites

(2010) Christoph D. Schmid et al.   PLoS One

Retroelements and their impact on genome evolution and functioning

(2009) Elena Gogvadze et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Human endogenous retrovirus HERV-K113 is capable of producing intact viral particles

(2008) K. Boller et al.   JOURNAL OF GENERAL VIROLOGY