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

Dicer-2-Dependent Generation of Viral DNA from Defective Genomes of RNA Viruses Modulates Antiviral Immunity in Insects

(2018) Enzo Z. Poirier et al.   Cell Host & Microbe

The evolutionary history of vertebrate RNA viruses

(2018) Mang Shi et al.   NATURE

Rewired RNAi-mediated genome surveillance in house dust mites

(2018) Mosharrof Mondal et al.   PLoS Genetics

Rapid Evolution of microRNA Loci in the Brown Algae

(2017) J. Mark Cock et al.   Genome Biology and Evolution

Human Virus-Derived Small RNAs Can Confer Antiviral Immunity in Mammals

(2017) Yang Qiu et al.   IMMUNITY

Autonomous Generation and Loading of DNA Guides by Bacterial Argonaute

(2017) Daan C. Swarts et al.   MOLECULAR CELL

Characterization of the piRNA pathway during development of the sea anemone Nematostella vectensis

(2017) Daniela Praher et al.   RNA Biology

Caenorhabditis elegans RIG-I Homolog Mediates Antiviral RNA Interference Downstream of Dicer-Dependent Biogenesis of Viral Small Interfering RNAs

(2017) Stephanie R. Coffman et al.   mBio

Questioning antiviral RNAi in mammals

(2017) Benjamin R. tenOever   Nature Microbiology

Reply to ‘Questioning antiviral RNAi in mammals’

(2017) Kate L. Jeffrey et al.   Nature Microbiology

The evolutionary origin of plant and animal microRNAs

(2017) Yehu Moran 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

The Evolution of Antiviral Defense Systems

(2016) Benjamin R. tenOever   Cell Host & Microbe

Deep sequencing of mycovirus-derived small RNAs from Botrytis species

(2016) Livia Donaire et al.   MOLECULAR PLANT PATHOLOGY

Redefining the invertebrate RNA virosphere

(2016) Mang Shi et al.   NATURE

miRNA Repertoires of Demosponges Stylissa carteri and Xestospongia testudinaria

(2016) Yi Jin Liew et al.   PLoS One

One Loop to Rule Them All: The Ping-Pong Cycle and piRNA-Guided Silencing

(2016) Benjamin Czech et al.   TRENDS IN BIOCHEMICAL SCIENCES

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Small RNA-Based Antiviral Defense in the Phytopathogenic Fungus Colletotrichum higginsianum

(2016) Sonia Campo et al.   PLoS Pathogens

Diverse Evolutionary Trajectories for Small RNA Biogenesis Genes in the Oomycete Genus Phytophthora

(2016) Stephanie R. Bollmann et al.   Frontiers in Plant Science

The miRNA biogenesis in marine bivalves

(2016) Umberto Rosani et al.   PeerJ

Induction and suppression of antiviral RNA interference by influenza A virus in mammalian cells

(2016) Yang Li et al.   Nature Microbiology

Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle

(2016) Takeshi Takeuchi et al.   Zoological Letters

Endogenous siRNAs and piRNAs derived from transposable elements and genes in the malaria vector mosquito Anopheles gambiae

(2015) Inna Biryukova et al.   BMC GENOMICS

Molecular evolution and diversification of the Argonaute family of proteins in plants

(2015) Ravi K Singh et al.   BMC PLANT BIOLOGY

An integrated transcriptomic and proteomic analysis of sea star epidermal secretions identifies proteins involved in defense and adhesion

(2015) Elise Hennebert et al.   Journal of Proteomics

Viral Small-RNA Analysis of Bombyx mori Larval Midgut during Persistent and Pathogenic Cytoplasmic Polyhedrosis Virus Infection

(2015) Aris Zografidis et al.   JOURNAL OF VIROLOGY

Ancient Origin and Recent Innovations of RNA Polymerase IV and V

(2015) Yi Huang et al.   MOLECULAR BIOLOGY AND EVOLUTION

The expanding world of small RNAs in plants

(2015) Filipe Borges et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Distinct sets of PIWI proteins produce arbovirus and transposon-derived piRNAs inAedes aegyptimosquito cells

(2015) Pascal Miesen et al.   NUCLEIC ACIDS RESEARCH

New animal phylogeny: future challenges for animal phylogeny in the age of phylogenomics

(2015) Gonzalo Giribet   ORGANISMS DIVERSITY & EVOLUTION

Comprehensive Annotation ofPhyscomitrella patensSmall RNA Loci Reveals That the Heterochromatic Short Interfering RNA Pathway Is Largely Conserved in Land Plants

(2015) Ceyda Coruh et al.   PLANT CELL

Dual functions of Macpiwi1 in transposon silencing and stem cell maintenance in the flatwormMacrostomum lignano

(2015) Xin Zhou et al.   RNA

Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response

(2015) Asiel Arturo Benitez et al.   Cell Reports

Ancient and Novel Small RNA Pathways Compensate for the Loss of piRNAs in Multiple Independent Nematode Lineages

(2015) Peter Sarkies et al.   PLOS BIOLOGY

The Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster

(2015) Claire L. Webster et al.   PLOS BIOLOGY

Roles and Programming of Arabidopsis ARGONAUTE Proteins during Turnip Mosaic Virus Infection

(2015) Hernan Garcia-Ruiz et al.   PLoS Pathogens

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

RNA interference-mediated antiviral defense in insects

(2015) Don B Gammon et al.   Current Opinion in Insect Science

The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum

(2014) Alessandra Rogato et al.   BMC GENOMICS

Replication of Many Human Viruses Is Refractory to Inhibition by Endogenous Cellular MicroRNAs

(2014) Hal P. Bogerd et al.   JOURNAL OF VIROLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The evolutionary journey of Argonaute proteins

(2014) Daan C Swarts et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Induction and suppression of tick cell antiviral RNAi responses by tick-borne flaviviruses

(2014) Esther Schnettler et al.   NUCLEIC ACIDS RESEARCH

Phylogenetic Analysis of the Endoribonuclease Dicer Family

(2014) Zeqian Gao et al.   PLoS One

Characterization of viral siRNA populations in honey bee colony collapse disorder

(2014) Nor Chejanovsky et al.   VIROLOGY

The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing

(2014) Simone Backes et al.   Cell Reports

The long and short of antiviral defense: small RNA-based immunity in insects

(2014) Alfred W Bronkhorst et al.   Current Opinion in Virology

Euchromatic Transposon Insertions Trigger Production of Novel Pi- and Endo-siRNAs at the Target Sites in the Drosophila Germline

(2014) Sergey Shpiz et al.   PLoS Genetics

piRNA clusters and open chromatin structure

(2014) Soichiro Yamanaka et al.   Mobile DNA

Classification and Comparison of Small RNAs from Plants

(2013) Michael J. Axtell   Annual Review of Plant Biology

RNAi pathways in the recognition of foreign RNA: antiviral responses and host–parasite interactions in nematodes: Figure 1

(2013) Peter Sarkies et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Functional diversification of Argonautes in nematodes: an expanding universe: Figure 1

(2013) Amy H. Buck et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure

(2013) Eiichi Shoguchi et al.   CURRENT BIOLOGY

Small RNAs tackle large viruses: RNA interference-based antiviral defense against DNA viruses in insects

(2013) Alfred W Bronkhorst et al.   FLY

Functional Diversity of RNAi-Associated sRNAs in Fungi

(2013) Francisco Nicolás et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Genetic Makeup of the Drosophila piRNA Pathway

(2013) Dominik Handler et al.   MOLECULAR CELL

Evolution of RNA interference proteins dicer and argonaute in Basidiomycota

(2013) Yang Hu et al.   MYCOLOGIA

RNA-mediated interference and reverse transcription control the persistence of RNA viruses in the insect model Drosophila

(2013) Bertsy Goic et al.   NATURE IMMUNOLOGY

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

RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond

(2013) Stephane E. Castel et al.   NATURE REVIEWS GENETICS

De novo piRNA cluster formation in the Drosophila germ line triggered by transgenes containing a transcribed transposon fragment

(2013) Ivan Olovnikov et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

PIWI proteins and PIWI-interacting RNAs function in Hydra somatic stem cells

(2013) C. E. Juliano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA Interference Functions as an Antiviral Immunity Mechanism in Mammals

(2013) Y. Li et al.   SCIENCE

Antiviral RNA Interference in Mammalian Cells

(2013) P. V. Maillard et al.   SCIENCE

Identification of RNase L-Dependent, 3'-End-Modified, Viral Small RNAs in Sindbis Virus-Infected Mammalian Cells

(2013) E. Girardi et al.   mBio

New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing

(2013) Alexander Maxwell Burroughs et al.   Wiley Interdisciplinary Reviews-RNA

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

(2013) Alyson Ashe et al.   eLife

RNA Interference Pathways in Fungi: Mechanisms and Functions

(2012) Shwu-Shin Chang et al.   Annual Review of Microbiology

C. elegans piRNAs Mediate the Genome-wide Surveillance of Germline Transcripts

(2012) Heng-Chi Lee et al.   CELL

A Role for Neuronal piRNAs in the Epigenetic Control of Memory-Related Synaptic Plasticity

(2012) Priyamvada Rajasethupathy et al.   CELL

Insights into the antiviral functions of the RNAi machinery in penaeid shrimp

(2012) Yannick Labreuche et al.   FISH & SHELLFISH IMMUNOLOGY

Delivery of dsRNA for RNAi in insects: an overview and future directions

(2012) Na Yu et al.   Insect Science

Evolution of Animal and Plant Dicers: Early Parallel Duplications and Recurrent Adaptation of Antiviral RNA Binding in Plants

(2012) Krishanu Mukherjee et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence

(2012) Yuval Tabach et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Arbovirus-Derived piRNAs Exhibit a Ping-Pong Signature in Mosquito Cells

(2012) Nicolas Vodovar et al.   PLoS One

Transposable-Element Associated Small RNAs in Bombyx mori Genome

(2012) Yimei Cai et al.   PLoS One

Convergent Evolution of Argonaute-2 Slicer Antagonism in Two Distinct Insect RNA Viruses

(2012) Joël T. van Mierlo et al.   PLoS Pathogens

Production of Virus-Derived Ping-Pong-Dependent piRNA-like Small RNAs in the Mosquito Soma

(2012) Elaine M. Morazzani et al.   PLoS Pathogens

RNAi in Arthropods: Insight into the Machinery and Applications for Understanding the Pathogen-Vector Interface

(2012) Annette-Christi Barnard et al.   Genes

RNA interference in marine and freshwater sponges: actin knockdown in Tethya wilhelma and Ephydatia muelleri by ingested dsRNA expressing bacteria

(2011) Ajna S Rivera et al.   BMC BIOTECHNOLOGY

The mosquito Aedes aegypti has a large genome size and high transposable element load but contains a low proportion of transposon-specific piRNAs

(2011) Peter Arensburger et al.   BMC GENOMICS

RNA Interference in Fungi: Pathways, Functions, and Applications

(2011) Yunkun Dang et al.   EUKARYOTIC CELL

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Compatibility with Killer Explains the Rise of RNAi-Deficient Fungi

(2011) I. A. Drinnenberg et al.   SCIENCE

Evidence for an instructive role of apoptosis during the metamorphosis of Hydractinia echinata (Hydrozoa)

(2011) Karola Wittig et al.   ZOOLOGY

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

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

Stem cell system in asexual and sexual reproduction of Enchytraeus japonensis (Oligochaeta, Annelida)

(2010) Chikako Yoshida-Noro et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Somatic stem cells express Piwi and Vasa genes in an adult ctenophore: Ancient association of “germline genes” with stemness

(2010) Alexandre Alié et al.   DEVELOPMENTAL BIOLOGY

Piwi expression in archeocytes and choanocytes in demosponges: insights into the stem cell system in demosponges

(2010) Noriko Funayama et al.   EVOLUTION & DEVELOPMENT

Exposure to dsRNA Elicits RNA Interference in Brachionus manjavacas (Rotifera)

(2010) Terry W. Snell et al.   MARINE BIOTECHNOLOGY

The Ectocarpus genome and the independent evolution of multicellularity in brown algae

(2010) J. Mark Cock et al.   NATURE

Influenza A virus-generated small RNAs regulate the switch from transcription to replication

(2010) J. T. Perez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Target RNA-Directed Trimming and Tailing of Small Silencing RNAs

(2010) S. L. Ameres et al.   SCIENCE

Endogenous Viral Elements in Animal Genomes

(2010) Aris Katzourakis et al.   PLoS Genetics

Retention and Loss of RNA Interference Pathways in Trypanosomatid Protozoans

(2010) Lon-Fye Lye et al.   PLoS Pathogens

Six RNA Viruses and Forty-One Hosts: Viral Small RNAs and Modulation of Small RNA Repertoires in Vertebrate and Invertebrate Systems

(2010) Poornima Parameswaran et al.   PLoS Pathogens

In vivoRNA interference in oyster -vasasilencing inhibits germ cell development

(2009) Caroline Fabioux et al.   FEBS Journal

Antiviral immunity in crustaceans

(2009) Haipeng Liu et al.   FISH & SHELLFISH IMMUNOLOGY

The role of RNAi and microRNAs in animal virus replication and antiviral immunity

(2009) J. L. Umbach et al.   GENES & DEVELOPMENT

Multiple Dicer Genes in the Early-Diverging Metazoa

(2009) D. de Jong et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular genetics and comparative genomics reveal RNAi is not functional in malaria parasites

(2009) Jake Baum et al.   NUCLEIC ACIDS RESEARCH

RNAi in Budding Yeast

(2009) I. A. Drinnenberg et al.   SCIENCE

Specificity of ARGONAUTE7-miR390 Interaction and Dual Functionality in TAS3 Trans-Acting siRNA Formation

(2008) Taiowa A. Montgomery et al.   CELL

The Pathway via D-Galacturonate/L-Galactonate Is Significant for Ascorbate Biosynthesis inEuglena gracilis

(2008) Takahiro Ishikawa et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Characterization of Hypovirus-Derived Small RNAs Generated in the Chestnut Blight Fungus by an Inducible DCL-2-Dependent Pathway

(2008) X. Zhang et al.   JOURNAL OF VIROLOGY

Piwi and piRNAs Act Upstream of an Endogenous siRNA Pathway to Suppress Tc3 Transposon Mobility in the Caenorhabditis elegans Germline

(2008) Partha P. Das et al.   MOLECULAR CELL

Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals

(2008) Andrew Grimson et al.   NATURE

An endogenous small interfering RNA pathway in Drosophila

(2008) Benjamin Czech et al.   NATURE

The evolution of RNAi as a defence against viruses and transposable elements

(2008) D. J Obbard et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ordered progression of nematogenesis from stem cells through differentiation stages in the tentacle bulb of Clytia hemisphaerica (Hydrozoa, Cnidaria)

(2007) Elsa Denker et al.   DEVELOPMENTAL BIOLOGY