Discovery of Replicating Circular RNAs by RNA-Seq and Computational Algorithms

Viroids: Survivors from the RNA World?

(2014) Ricardo Flores et al.   Annual Review of Microbiology

Survey and analysis of simple sequence repeats (SSRs) present in the genomes of plant viroids

(2014) Lü Qin et al.   FEBS Open Bio

Characterization of a new apscaviroid from American persimmon

(2013) Takao Ito et al.   ARCHIVES OF VIROLOGY

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

Search strategy has influenced the discovery rate of human viruses

(2013) Ronald Rosenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Viroids: How to infect a host and cause disease without encoding proteins

(2012) Beatriz Navarro et al.   BIOCHIMIE

Dahlia latent viroid: a recombinant new species of the family Pospiviroidae posing intriguing questions about its origin and classification

(2012) J. T. J. Verhoeven et al.   JOURNAL OF GENERAL VIROLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm

(2012) Q. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Viroid-specific small RNA in plant disease

(2012) Christian Hammann et al.   RNA Biology

Circular RNAs are abundant, conserved, and associated with ALU repeats

(2012) W. R. Jeck et al.   RNA

Comprehensive diversity analysis of viroids infecting grapevine in China and Japan

(2012) Dongmei Jiang et al.   VIRUS RESEARCH

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Whole-transcriptome RNAseq analysis from minute amount of total RNA

(2011) Muhammad A. Tariq et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-wide discovery of circular RNAs in Archaea

(2011) Miri Danan et al.   NUCLEIC ACIDS RESEARCH

Rolling-circle replication of viroids, viroid-like satellite RNAs and hepatitis delta virus: Variations on a theme

(2011) Ricardo Flores et al.   RNA Biology

Accumulation of Potato spindle tuber viroid-specific small RNAs is accompanied by specific changes in gene expression in two tomato cultivars

(2011) Ying Wang et al.   VIROLOGY

Virus-derived siRNAs and piRNAs in immunity and pathogenesis

(2011) Shou-Wei Ding et al.   Current Opinion in Virology

In-depth sequencing of the siRNAs associated with peach latent mosaic viroid infection

(2010) François Bolduc et al.   BMC MOLECULAR BIOLOGY

High-throughput sequencing ofHop stunt viroid-derived small RNAs from cucumber leaves and phloem

(2010) GERMAN MARTINEZ et al.   MOLECULAR PLANT PATHOLOGY

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs

(2010) Q. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Biology of Viroid-Host Interactions

(2009) Biao Ding   Annual Review of Phytopathology

Identification and characterization of a new coleviroid (CbVd-5)

(2009) Wan-Ying Hou et al.   ARCHIVES OF VIROLOGY

RNA-Dependent RNA Polymerase 6 Delays Accumulation and Precludes Meristem Invasion of a Viroid That Replicates in the Nucleus

(2009) F. Di Serio et al.   JOURNAL OF VIROLOGY

Deep Sequencing of the Small RNAs Derived from Two Symptomatic Variants of a Chloroplastic Viroid: Implications for Their Genesis and for Pathogenesis

(2009) Francesco Di Serio et al.   PLoS One

Deep Sequencing of Viroid-Derived Small RNAs from Grapevine Provides New Insights on the Role of RNA Silencing in Plant-Viroid Interaction

(2009) Beatriz Navarro et al.   PLoS One

Cultivated Grapevines Represent a Symptomless Reservoir for the Transmission of Hop Stunt Viroid to Hop Crops: 15 Years of Evolutionary Analysis

(2009) Yoko Kawaguchi-Ito et al.   PLoS One

Interplay between viroid-induced pathogenesis and RNA silencing pathways

(2009) Gustavo Gómez et al.   TRENDS IN PLANT SCIENCE

Satellite RNAs and Satellite Viruses of Plants

(2009) Chung-Chi Hu et al.   Viruses-Basel

Viroid Pathogenicity: One Process, Many Faces

(2009) Robert Owens et al.   Viruses-Basel

Mechanism of Induction and Suppression of Antiviral Immunity Directed by Virus-Derived Small RNAs in Drosophila

(2008) Roghiyh Aliyari et al.   Cell Host & Microbe

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

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

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

Poly A- Transcripts Expressed in HeLa Cells

(2008) Qingfa Wu et al.   PLoS One