Mouse B2 SINE elements function as IFN-inducible enhancers

Fumarate induces vesicular release of mtDNA to drive innate immunity

(2023) Vincent Zecchini et al.   NATURE

H3K9 trimethylation in active chromatin restricts the usage of functional CTCF sites in SINE B2 repeats

(2022) Francesco Gualdrini et al.   GENES & DEVELOPMENT

IFNγ Regulates NAD+ Metabolism to Promote the Respiratory Burst in Human Monocytes

(2022) Katelyn J McCann et al.   Blood Advances

Interferons reshape the 3D conformation and accessibility of macrophage chromatin

(2022) Ekaterini Platanitis et al.   iScience

Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity

(2022) Conor J. Kelly et al.   GENOME RESEARCH

Frequent aneuploidy in primary human T cells after CRISPR–Cas9 cleavage

(2022) Alessio David Nahmad et al.   NATURE BIOTECHNOLOGY

Evolution and antiviral activity of a human protein of retroviral origin

(2022) John A. Frank et al.   SCIENCE

Wildtype heterogeneity contributes to clonal variability in genome edited cells

(2022) Lukas Westermann et al.   Scientific Reports

Dicer represses the interferon response and the double-stranded RNA-activated protein kinase pathway in mouse embryonic stem cells

(2021) Chandan Gurung et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Dfam community resource of transposable element families, sequence models, and genome annotations

(2021) Jessica Storer et al.   Mobile DNA

B2 SINE Copies Serve as a Transposable Boundary of DNA Methylation and Histone Modifications in the Mouse

(2021) Tomoko Ichiyanagi et al.   MOLECULAR BIOLOGY AND EVOLUTION

An isoform of Dicer protects mammalian stem cells against multiple RNA viruses

(2021) Enzo Z. Poirier et al.   SCIENCE

Emerging roles for endogenous retroviruses in immune epigenetic regulation*

(2021) Carmen A. Buttler et al.   IMMUNOLOGICAL REVIEWS

Ensembl 2022

(2021) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Genetic mapping reveals Nfkbid as a central regulator of humoral immunity to Toxoplasma gondii

(2021) Scott P. Souza et al.   PLoS Pathogens

Transposable elements have contributed human regulatory regions that are activated upon bacterial infection

(2020) Lucia Bogdan et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The conserved herpesviral kinase ORF36 activates B2 retrotransposons during murine gammaherpesvirus infection

(2020) Aaron M. Schaller et al.   JOURNAL OF VIROLOGY

Dicing the Disease with Dicer: The Implications of Dicer Ribonuclease in Human Pathologies

(2020) Eleni I. Theotoki et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Efficient low-cost chromatin profiling with CUT&Tag

(2020) Hatice S. Kaya-Okur et al.   Nature Protocols

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

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

GENCODE 2021

(2020) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

The Histone Methyltransferase DOT1L Is Essential for Humoral Immune Responses

(2020) Liam Kealy et al.   Cell Reports

Genome-wide expression analysis of a new class of lncRNAs driven by SINE B2

(2020) Jinjiang Fan et al.   GENE

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

(2019) Uku Raudvere et al.   NUCLEIC ACIDS RESEARCH

A molecular switch from STAT2-IRF9 to ISGF3 underlies interferon-induced gene transcription

(2019) Ekaterini Platanitis et al.   Nature Communications

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

JASPAR 2020: update of the open-access database of transcription factor binding profiles

(2019) Oriol Fornes et al.   NUCLEIC ACIDS RESEARCH

B2 and ALU retrotransposons are self-cleaving ribozymes whose activity is enhanced by EZH2

(2019) Alfredo J. Hernandez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Ryan M Layer et al.   NATURE METHODS

Comparative Analysis of Immune Cells Reveals a Conserved Regulatory Lexicon

(2018) Elisa Donnard et al.   Cell Systems

Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation

(2018) Sergi Cuartero et al.   NATURE IMMUNOLOGY

Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences

(2018) Anqi Zhu et al.   BIOINFORMATICS

Genome-wide mapping of infection-induced SINE RNAs reveals a role in selective mRNA export

(2017) John Karijolich et al.   NUCLEIC ACIDS RESEARCH

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Co-option of endogenous viral sequences for host cell function

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

Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses

(2017) Andrew E. Shaw et al.   PLOS BIOLOGY

CDK9-dependent RNA polymerase II pausing controls transcription initiation

(2017) Saskia Gressel et al.   eLife

Dicer, a new regulator of pluripotency exit and LINE-1 elements in mouse embryonic stem cells

(2017) Maxime Bodak et al.   FEBS Open Bio

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

(2016) Philip Ewels et al.   BIOINFORMATICS

Regulatory activities of transposable elements: from conflicts to benefits

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

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

(2016) E. B. Chuong et al.   SCIENCE

IFN-γ Induces Histone 3 Lysine 27 Trimethylation in a Small Subset of Promoters to Stably Silence Gene Expression in Human Macrophages

(2016) Yu Qiao et al.   Cell Reports

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

(2015) Ying Jin et al.   BIOINFORMATICS

Getting up to speed with transcription elongation by RNA polymerase II

(2015) Iris Jonkers et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

CDK9 inhibitors define elongation checkpoints at both ends of RNA polymerase II–transcribed genes

(2015) Clélia Laitem et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CDK9 inhibitors define elongation checkpoints at both ends of RNA polymerase II–transcribed genes

(2015) Clélia Laitem et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Infection-Induced Retrotransposon-Derived Noncoding RNAs Enhance Herpesviral Gene Expression via the NF-κB Pathway

(2015) John Karijolich et al.   PLoS Pathogens

Widespread contribution of transposable elements to the innovation of gene regulatory networks

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

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

(2013) Y. Liao et al.   BIOINFORMATICS

Dicer's role as an antiviral: still an enigma

(2013) Christopher R MacKay et al.   CURRENT OPINION IN IMMUNOLOGY

Synergistic Activation of Inflammatory Cytokine Genes by Interferon-γ-Induced Chromatin Remodeling and Toll-like Receptor Signaling

(2013) Yu Qiao et al.   IMMUNITY

Paleovirology of 'syncytins', retroviral env genes exapted for a role in placentation

(2013) C. Lavialle et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Conservation and divergence in the transcriptional programs of the human and mouse immune systems

(2013) T. Shay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic responses in mouse models poorly mimic human inflammatory diseases

(2013) Junhee Seok et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rules of Engagement: Molecular Insights from Host-Virus Arms Races

(2012) Matthew D. Daugherty et al.   Annual Review of Genetics

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

(2012) Jian Ye et al.   BMC BIOINFORMATICS

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

Reduced DICER1 Elicits an Interferon Response in Endometrial Cancer Cells

(2012) K. B. Chiappinelli et al.   MOLECULAR CANCER RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Paleovirology and virally derived immunity

(2012) Amr Aswad et al.   TRENDS IN ECOLOGY & EVOLUTION

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Hsp70, a messenger from hyperthermia for the immune system

(2011) Anna Jolesch et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

I B kinase   (IKK ) regulates the balance between type I and type II interferon responses

(2011) S.-L. Ng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

Lysine methylation of the NF-κB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-κB signaling

(2010) Dan Levy et al.   NATURE IMMUNOLOGY

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

InvAluable junk: The cellular impact and function of Alu and B2 RNAs

(2009) Ryan D. Walters et al.   IUBMB LIFE

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes

(2009) P. Yakovchuk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Baseline Mechanical Characterization of J774 Macrophages

(2008) Jonathan Lam et al.   BIOPHYSICAL JOURNAL

Endogenous retroviruses

(2008) F. Arnaud et al.   CELLULAR AND MOLECULAR LIFE SCIENCES