Deep Sequencing of Small RNAs in Tomato for Virus and Viroid Identification and Strain Differentiation

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

Using small RNA sequences to diagnose, sequence, and investigate the infectivity characteristics of vegetable-infecting viruses

(2011) Charles Hagen et al.   ARCHIVES OF VIROLOGY

Multiple polyadenylated RNA viruses detected in pooled cultivated and wild plant samples

(2011) Stephen J. Wylie et al.   ARCHIVES OF VIROLOGY

Pathogen detection using short-RNA deep sequencing subtraction and assembly

(2011) O. Isakov et al.   BIOINFORMATICS

In Silico Reconstruction of Viral Genomes from Small RNAs Improves Virus-Derived Small Interfering RNA Profiling

(2011) N. Vodovar et al.   JOURNAL OF VIROLOGY

Emerging Viral Diseases of Tomato Crops

(2010) Inge M. Hanssen et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

First Report of Natural Infection of Greenhouse Tomatoes by Potato spindle tuber viroid in the United States

(2010) K.-S. Ling et al.   PLANT DISEASE

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

A Novel miRNA Processing Pathway Independent of Dicer Requires Argonaute2 Catalytic Activity

(2010) D. Cifuentes et al.   SCIENCE

Deep sequencing analysis of viruses infecting grapevines: Virome of a vineyard

(2010) Beatrix Coetzee et al.   VIROLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology

(2009) IAN P. ADAMS et al.   MOLECULAR PLANT PATHOLOGY

Pepino mosaic virus: a successful pathogen that rapidly evolved from emerging to endemic in tomato crops

(2009) INGE M. HANSSEN et al.   MOLECULAR PLANT PATHOLOGY

First Report of a Natural Infection by Mexican Papita Viroid and Tomato Chlorotic Dwarf Viroid on Greenhouse Tomatoes in Mexico

(2009) K.-S. Ling et al.   PLANT DISEASE

First Report of Mexican papita viroid Infecting Greenhouse Tomato in Canada

(2009) K.-S. Ling et al.   PLANT DISEASE

First Report of Tomato chlorotic dwarf viroid in Greenhouse Tomatoes in Arizona

(2009) K.-S. Ling et al.   PLANT DISEASE

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

Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus

(2009) M. Al Rwahnih et al.   VIROLOGY

Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: A generic method for diagnosis, discovery and sequencing of viruses

(2009) Jan F. Kreuze et al.   VIROLOGY

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

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

Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells

(2008) Yoshinori Kawamura et al.   NATURE

Genetic Composition of Pepino mosaic virus Population in North American Greenhouse Tomatoes

(2008) Kai-Shu Ling et al.   PLANT DISEASE

Small RNAs in viral infection and host defense

(2008) Sizolwenkosi Mlotshwa et al.   TRENDS IN PLANT SCIENCE

Evolution of plant microRNAs and their targets

(2008) Michael J. Axtell et al.   TRENDS IN PLANT SCIENCE