Functional Characterization of the Cnidarian Antiviral Immune Response Reveals Ancestral Complexity

Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri

(2020) Nathan J. Kenny et al.   Nature Communications

Kinetics of transcriptional response against poly (I:C) and infectious salmon anemia virus (ISAV) in Atlantic salmon kidney (ASK) cell line

(2020) Adriana Magalhães Santos Andresen et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

STING cyclic dinucleotide sensing originated in bacteria

(2020) Benjamin R. Morehouse et al.   NATURE

Prokaryotic viperins produce diverse antiviral molecules

(2020) Aude Bernheim et al.   NATURE

TATA Binding Protein (TBP) Promoter Drives Ubiquitous Expression of Marker Transgene in the Adult Sea Anemone Nematostella vectensis

(2020) Yael Admoni et al.   Genes

Palaeoclimate ocean conditions shaped the evolution of corals and their skeletons through deep time

(2020) Andrea M. Quattrini et al.   Nature Ecology & Evolution

Unravelling the developmental and functional significance of an ancient Argonaute duplication

(2020) Arie Fridrich et al.   Nature Communications

Electroporation of short hairpin RNAs for rapid and efficient gene knockdown in the starlet sea anemone, Nematostella vectensis

(2019) Ahmet Karabulut et al.   DEVELOPMENTAL BIOLOGY

The Molecular Basis of Viral Inhibition of IRF- and STAT-Dependent Immune Responses

(2019) Hao-Sen Chiang et al.   Frontiers in Immunology

CirGO: an alternative circular way of visualising gene ontology terms

(2019) Irina Kuznetsova et al.   BMC BIOINFORMATICS

MicroRNA transcriptome analysis of poly I:C-stimulated and PRRSV-infected porcine alveolar macrophages

(2019) Junjing Wu et al.   JOURNAL OF APPLIED GENETICS

Cyclic GMP–AMP signalling protects bacteria against viral infection

(2019) Daniel Cohen et al.   NATURE

A conserved miRNA-183 cluster regulates the innate antiviral response

(2019) Ragunath Singaravelu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CDD/SPARCLE: the conserved domain database in 2020

(2019) Shennan Lu et al.   NUCLEIC ACIDS RESEARCH

The ETS transcription factor ELF1 regulates a broadly antiviral program distinct from the type I interferon response

(2019) Leon Louis Seifert et al.   PLoS Pathogens

The Dicer from oyster Crassostrea gigas functions as an intracellular recognition molecule and effector in anti-viral immunity

(2019) Xiaojing Lv et al.   FISH & SHELLFISH IMMUNOLOGY

RIG-I Recognition of RNA Targets: The Influence of Terminal Base Pair Sequence and Overhangs on Affinity and Signaling

(2019) Xiaoming Ren et al.   Cell Reports

A conserved interferon regulation factor 1 (IRF-1) from Pacific oyster Crassostrea gigas functioned as an activator of IFN pathway

(2018) Mengmeng Lu et al.   FISH & SHELLFISH IMMUNOLOGY

Dynamics of venom composition across a complex life cycle

(2018) Yaara Y Columbus-Shenkar et al.   eLife

The Diverse Roles of microRNAs at the Host–Virus Interface

(2018) Annie Bernier et al.   Viruses-Basel

Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes

(2018) Fergal M. Waldron et al.   PLoS Genetics

Gene expression variability across cells and species shapes innate immunity

(2018) Tzachi Hagai et al.   NATURE

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Meganuclease-assisted generation of stable transgenics in the sea anemone Nematostella vectensis

(2017) Eduard Renfer et al.   Nature Protocols

Sea anemone model has a single Toll-like receptor that can function in pathogen detection, NF-κB signal transduction, and development

(2017) Joseph J. Brennan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome-wide analysis of immune-responsive microRNAs against poly (I:C) challenge in Branchiostoma belcheri by deep sequencing and bioinformatics

(2017) Qi-Lin Zhang et al.   Oncotarget

The evolutionary origin of plant and animal microRNAs

(2017) Yehu Moran et al.   Nature Ecology & Evolution

Ctenophore relationships and their placement as the sister group to all other animals

(2017) Nathan V. Whelan et al.   Nature Ecology & Evolution

Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements

(2017) Samuel H. Lewis et al.   Nature Ecology & Evolution

Characterization of the Mollusc RIG-I/MAVS Pathway Reveals an Archaic Antiviral Signalling Framework in Invertebrates

(2017) Baoyu Huang et al.   Scientific Reports

Importance of Nucleic Acid Recognition in Inflammation and Autoimmunity

(2016) Franck J. Barrat et al.   Annual Review of Medicine

The Evolution of Antiviral Defense Systems

(2016) Benjamin R. tenOever   Cell Host & Microbe

Gene expression profile after activation of RIG-I in 5'ppp-dsRNA challenged DF1

(2016) Yang Chen et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

The rise of the starlet sea anemone Nematostella vectensis as a model system to investigate development and regeneration

(2016) Michael J. Layden et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Transcriptome analysis reveals strong and complex antiviral response in a mollusc

(2015) Yan He et al.   FISH & SHELLFISH IMMUNOLOGY

A Conserved Histidine in the RNA Sensor RIG-I Controls Immune Tolerance to N1-2′O-Methylated Self RNA

(2015) Christine Schuberth-Wagner et al.   IMMUNITY

Influenza A Virus Panhandle Structure Is Directly Involved in RIG-I Activation and Interferon Induction

(2015) GuanQun Liu et al.   JOURNAL OF VIROLOGY

The making of an embryo in a basal metazoan: Proteomic analysis in the sea anemoneNematostella vectensis

(2015) Shimrit Levitan et al.   PROTEOMICS

Interferon-Stimulated Genes: A Complex Web of Host Defenses

(2014) William M. Schneider et al.   Annual Review of Immunology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

MDA5 and LGP2: Accomplices and Antagonists of Antiviral Signal Transduction

(2014) K. R. Rodriguez et al.   JOURNAL OF VIROLOGY

Activation of the RIG-I Pathway during Influenza Vaccination Enhances the Germinal Center Reaction, Promotes T Follicular Helper Cell Induction, and Provides a Dose-Sparing Effect and Protective Immunity

(2014) R. R. Kulkarni et al.   JOURNAL OF VIROLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Antiviral immunity via RIG-I-mediated recognition of RNA bearing 5′-diphosphates

(2014) Delphine Goubau et al.   NATURE

Dicer-related helicase 3 forms an obligate dimer for recognizing 22G-RNA

(2014) Megan E. Fitzgerald et al.   NUCLEIC ACIDS RESEARCH

Toll-Like Receptor Signaling Pathways

(2014) Takumi Kawasaki et al.   Frontiers in Immunology

Characterization of differential transcript abundance through time during Nematostella vectensis development

(2013) Rebecca Helm et al.   BMC GENOMICS

RIG-I activation inhibits HIV replication in macrophages

(2013) Yizhong Wang et al.   JOURNAL OF LEUKOCYTE BIOLOGY

The Evolution of MicroRNA Pathway Protein Components in Cnidaria

(2013) Yehu Moran et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancient Origins of Vertebrate-Specific Innate Antiviral Immunity

(2013) Krishanu Mukherjee et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Homologous RIG-I-like helicase proteins direct RNAi-mediated antiviral immunity in C. elegans by distinct mechanisms

(2013) X. Guo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A virocentric perspective on the evolution of life

(2013) Eugene V Koonin et al.   Current Opinion in Virology

A deletion polymorphism in the Caenorhabditis elegans RIG-I homolog disables viral RNA dicing and antiviral immunity

(2013) Alyson Ashe et al.   eLife

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Kinetic mechanism for viral dsRNA length discrimination by MDA5 filaments

(2012) A. Peisley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Evolutionary crossroads in developmental biology: Cnidaria

(2011) U. Technau et al.   DEVELOPMENT

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

High Cleavage Efficiency of a 2A Peptide Derived from Porcine Teschovirus-1 in Human Cell Lines, Zebrafish and Mice

(2011) Jin Hee Kim et al.   PLoS One

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes

(2011) Maria Anisimova et al.   SYSTEMATIC BIOLOGY

Natural and Experimental Infection of Caenorhabditis Nematodes by Novel Viruses Related to Nodaviruses

(2011) Marie-Anne Félix et al.   PLOS BIOLOGY

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

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

Double-stranded RNA-dependent ATPase DRH-3

(2010) Christian Matranga et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Antiviral Response Dictated by Choreographed Cascade of Transcription Factors

(2010) E. Zaslavsky et al.   JOURNAL OF IMMUNOLOGY

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Origin and evolution of the RIG-I like RNA helicase gene family

(2009) Jun Zou et al.   BMC EVOLUTIONARY BIOLOGY

Recognition of 5′ Triphosphate by RIG-I Helicase Requires Short Blunt Double-Stranded RNA as Contained in Panhandle of Negative-Strand Virus

(2009) Martin Schlee et al.   IMMUNITY

Activation of MDA5 Requires Higher-Order RNA Structures Generated during Virus Infection

(2009) A. Pichlmair et al.   JOURNAL OF VIROLOGY

5'-triphosphate RNA requires base-paired structures to activate antiviral signaling via RIG-I

(2009) A. Schmidt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A muscle-specific transgenic reporter line of the sea anemone, Nematostella vectensis

(2009) E. Renfer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An RIG-I-Like RNA Helicase Mediates Antiviral RNAi Downstream of Viral siRNA Biogenesis in Caenorhabditis elegans

(2009) Rui Lu et al.   PLoS Pathogens

Two strategies for gene regulation by promoter nucleosomes

(2008) I. Tirosh et al.   GENOME RESEARCH

Length-dependent recognition of double-stranded ribonucleic acids by retinoic acid–inducible gene-I and melanoma differentiation–associated gene 5

(2008) Hiroki Kato et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Evolution of MDA-5/RIG-I-dependent innate immunity: Independent evolution by domain grafting

(2008) D. Sarkar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA