Functional lability of RNA-dependent RNA polymerases in animals

RNA Dependent RNA Polymerases: Insights from Structure, Function and Evolution

(2018) Sangita Venkataraman et al.   Viruses-Basel

The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology

(2018) Yu Fu et al.   eLife

Amphioxus functional genomics and the origins of vertebrate gene regulation

(2018) Ferdinand Marlétaz et al.   NATURE

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms

(2017) Javier Tapial et al.   GENOME RESEARCH

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

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

Systemic RNAi in western corn rootworm, Diabrotica virgifera virgifera , does not involve transitive pathways

(2016) Huarong Li et al.   Insect Science

Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases

(2016) Xinlei Qian et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genetic and mechanistic diversity of piRNA 3′-end formation

(2016) Rippei Hayashi et al.   NATURE

Nascent RNA sequencing reveals distinct features in plant transcription

(2016) Jonathan Hetzel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An RNA-dependent RNA polymerase gene in bat genomes derived from an ancient negative-strand RNA virus

(2016) Masayuki Horie et al.   Scientific Reports

The exonuclease Nibbler regulates age-associated traits and modulates piRNA length inDrosophila

(2015) Virzhiniya L. Feltzin et al.   AGING CELL

Antagonistic roles of Nibbler and Hen1 in modulating piRNA 3′ ends inDrosophila

(2015) Hui Wang et al.   DEVELOPMENT

A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway

(2015) Mark A. Miller et al.   Evolutionary Bioinformatics

Traces of ATCV-1 associated with laboratory component contamination

(2015) Kristín Rós Kjartansdóttir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reply to Kjartansdóttir et al.: Chlorovirus ATCV-1 findings not explained by contamination

(2015) Robert H. Yolken et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNAi and Heterochromatin Assembly

(2015) Robert Martienssen et al.   Cold Spring Harbor Perspectives in Biology

Cnidarian microRNAs frequently regulate targets by cleavage

(2014) Y. Moran et al.   GENOME RESEARCH

Chlorovirus ATCV-1 is part of the human oropharyngeal virome and is associated with changes in cognitive functions in humans and mice

(2014) Robert H. Yolken et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Two apextrin-like proteins mediate extracellular and intracellular bacterial recognition in amphioxus

(2014) Guangrui Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

How much does the amphioxus genome represent the ancestor of chordates?

(2012) A. Louis et al.   Briefings in Functional Genomics

A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals

(2012) Roselyne M. Labbé et al.   STEM CELLS

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

The Caenorhabditis elegans HEN1 Ortholog, HENN-1, Methylates and Stabilizes Select Subclasses of Germline Small RNAs

(2012) Allison C. Billi et al.   PLoS Genetics

PIWI Associated siRNAs and piRNAs Specifically Require the Caenorhabditis elegans HEN1 Ortholog henn-1

(2012) Taiowa A. Montgomery et al.   PLoS Genetics

Differential Impact of the HEN1 Homolog HENN-1 on 21U and 26G RNAs in the Germline of Caenorhabditis elegans

(2012) Leonie M. Kamminga et al.   PLoS Genetics

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

The Exoribonuclease Nibbler Controls 3′ End Processing of MicroRNAs in Drosophila

(2011) Nan Liu et al.   CURRENT BIOLOGY

The 3′-to-5′ Exoribonuclease Nibbler Shapes the 3′ Ends of MicroRNAs Bound to Drosophila Argonaute1

(2011) Bo W. Han et al.   CURRENT BIOLOGY

Evolutionary crossroads in developmental biology: amphioxus

(2011) S. Bertrand et al.   DEVELOPMENT

Select microRNAs are essential for early development in the sea urchin

(2011) Jia L. Song et al.   DEVELOPMENTAL BIOLOGY

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing

(2011) R. Sanchez et al.   NUCLEIC ACIDS RESEARCH

Hen1 is required for oocyte development and piRNA stability in zebrafish

(2010) Leonie M Kamminga et al.   EMBO JOURNAL

Structural basis for 5′-nucleotide base-specific recognition of guide RNA by human AGO2

(2010) Filipp Frank et al.   NATURE

Distinct RNA-dependent RNA polymerases are required for RNAi triggered by double-stranded RNA versus truncated transgenes in Paramecium tetraurelia

(2010) Simone Marker et al.   NUCLEIC ACIDS RESEARCH

Sequential rounds of RNA-dependent RNA transcription drive endogenous small-RNA biogenesis in the ERGO-1/Argonaute pathway

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

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

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

Regulation of gene expression via the core promoter and the basal transcriptional machinery

(2009) Tamar Juven-Gershon et al.   DEVELOPMENTAL BIOLOGY

Evolution of the RNA-dependent RNA polymerase (RdRP) genes: Duplications and possible losses before and after the divergence of major eukaryotic groups

(2009) Jie Zong et al.   GENE

Distinct Argonaute-Mediated 22G-RNA Pathways Direct Genome Surveillance in the C. elegans Germline

(2009) Weifeng Gu et al.   MOLECULAR CELL

An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA

(2009) Yoshiko Maida et al.   NATURE

Structural insights into mechanisms of the small RNA methyltransferase HEN1

(2009) Ying Huang et al.   NATURE

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

26G endo-siRNAs regulate spermatogenic and zygotic gene expression in Caenorhabditis elegans

(2009) T. Han et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution profiling and discovery of planarian small RNAs

(2009) Marc R. Friedländer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway

(2009) M. Ghildiyal et al.   RNA

Sorting of Small RNAs into Arabidopsis Argonaute Complexes Is Directed by the 5′ Terminal Nucleotide

(2008) Shijun Mi et al.   CELL

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

(2008) Taiowa A. Montgomery et al.   CELL

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

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

(2008) Andrew Grimson et al.   NATURE

The Mechanism Selecting the Guide Strand from Small RNA Duplexes is Different Among Argonaute Proteins

(2008) Atsushi Takeda et al.   PLANT AND CELL PHYSIOLOGY

Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells

(2008) M. Ghildiyal et al.   SCIENCE

Use, tolerance and avoidance of amplified RNA silencing by plants

(2008) Olivier Voinnet   TRENDS IN PLANT SCIENCE