Going beyond consensus genome sequences: An innovative SNP-based methodology reconstructs different Ugandan cassava brown streak virus haplotypes at a nationwide scale in Rwanda

Strong selection and high mutation supply characterize experimental Chlorovirus evolution

(2022) Cas Retel et al.   Virus Evolution

Detection of Banana Mild Mosaic Virus in Musa In Vitro Plants: High-Throughput Sequencing Presents Higher Diagnostic Sensitivity Than (IC)-RT-PCR and Identifies a New Betaflexiviridae Species

(2022) Marwa Hanafi et al.   Plants-Basel

Risk factors associated with cassava brown streak disease dissemination through seed pathways in Eastern D.R. Congo

(2022) Yves Kwibuka et al.   Frontiers in Plant Science

Detection of Four New Tomato Viruses in Serbia using Post-Hoc High-Throughput Sequencing Analysis of Samples from a Large-Scale Field Survey

(2021) Ana Vucurovic et al.   PLANT DISEASE

The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe

(2021) Megan A Wallace et al.   Virus Evolution

Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation

(2021) Catherine D. Aimone et al.   JOURNAL OF GENERAL VIROLOGY

Comparison of high throughput sequencing to standard protocols for virus detection in berry crops

(2021) Dan Edward Veloso Villamor et al.   PLANT DISEASE

Novel Ampeloviruses Infecting Cassava in Central Africa and the South-West Indian Ocean Islands

(2021) Yves Kwibuka et al.   Viruses-Basel

Evolutionary study of maize dwarf mosaic virus using nearly complete genome sequences acquired by next-generation sequencing

(2021) Dulanjani Wijayasekara et al.   Scientific Reports

Phylogenetics and Evolution of Potato Virus V: Another Potyvirus that Originated in the Andes

(2021) Segundo Fuentes et al.   PLANT DISEASE

Integrating High throughput Sequencing into Survey Design Reveals Turnip Yellows Virus and Soybean Dwarf Virus in Pea (Pisum Sativum) in the United Kingdom

(2021) Aimee R. Fowkes et al.   Viruses-Basel

Reconsidering causal association in plant virology

(2020) Adrian Fox   PLANT PATHOLOGY

Transmission modes affect the population structure of potato virus Y in potato

(2020) Washington da Silva et al.   PLoS Pathogens

Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales

(2020) François Maclot et al.   Frontiers in Microbiology

rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data

(2019) Elena Bushmanova et al.   GigaScience

Cassava Brown Streak Disease and Ugandan cassava brown streak virus Reported for the First Time in Zambia

(2018) Rabson M. Mulenga et al.   PLANT DISEASE

Evaluation of Six Methods for Extraction of Total RNA from Loquat

(2018) Zhang LING et al.   Notulae Botanicae Horti Agrobotanici Cluj-Napoca

Why are RNA virus mutation rates so damn high?

(2018) Siobain Duffy   PLOS BIOLOGY

Honey bee-assisted surveillance for early plant virus detection

(2018) John M. K. Roberts et al.   ANNALS OF APPLIED BIOLOGY

The role of the whitefly, Bemisia tabaci (Gennadius), and farmer practices in the spread of cassava brown streak ipomoviruses

(2017) Midatharahally N. Maruthi et al.   JOURNAL OF PHYTOPATHOLOGY

Cassava brown streak disease: historical timeline, current knowledge and future prospects

(2017) Katie R. Tomlinson et al.   MOLECULAR PLANT PATHOLOGY

Cassava brown streak disease in Rwanda, the associated viruses and disease phenotypes

(2017) E. Munganyinka et al.   PLANT PATHOLOGY

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data: Table 1.

(2015) Chase W. Nelson et al.   BIOINFORMATICS

Temporal Dynamics of Intrahost Molecular Evolution for a Plant RNA Virus

(2015) José M. Cuevas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Group Selection and Contribution of Minority Variants during Virus Adaptation Determines Virus Fitness and Phenotype

(2015) Antonio V. Bordería et al.   PLoS Pathogens

Population genomics of intrapatient HIV-1 evolution

(2015) Fabio Zanini et al.   eLife

Current impact and future directions of high throughput sequencing in plant virus diagnostics

(2014) Sebastien Massart et al.   VIRUS RESEARCH

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Low frequency clonal mutations recoverable by deep sequencing in patients with aplastic anemia

(2013) A A Lane et al.   LEUKEMIA

Validation of SNP Allele Frequencies Determined by Pooled Next-Generation Sequencing in Natural Populations of a Non-Model Plant Species

(2013) Christian Rellstab et al.   PLoS One

Correction: Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Provides Insight into the Origins of an Emergent Plant Disease

(2013) Honour C. McCann et al.   PLoS Pathogens

Deep sequencing reveals persistence of intra- and inter-host genetic diversity in natural and greenhouse populations of zucchini yellow mosaic virus

(2012) H. E. Simmons et al.   JOURNAL OF GENERAL VIROLOGY

Coat proteins, host factors and plant viral replication

(2012) Konstantin I Ivanov et al.   Current Opinion in Virology

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler et al.   BIOINFORMATICS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Comparing the regional epidemiology of the cassava mosaic and cassava brown streak virus pandemics in Africa

(2011) J.P. Legg et al.   VIRUS RESEARCH

Screening Low-Frequency SNPS From Genome-Wide Association Study Reveals a New Risk Allele for Progression to AIDS

(2010) Sigrid Le Clerc et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Analysis of cassava brown streak viruses reveals the presence of distinct virus species causing cassava brown streak disease in East Africa

(2010) S. Winter et al.   JOURNAL OF GENERAL VIROLOGY

Evolution of cassava brown streak disease-associated viruses

(2010) D. R. Mbanzibwa et al.   JOURNAL OF GENERAL VIROLOGY

Simultaneous virus-specific detection of the two cassava brown streak-associated viruses by RT-PCR reveals wide distribution in East Africa, mixed infections, and infections in Manihot glaziovii

(2010) D.R. Mbanzibwa et al.   JOURNAL OF VIROLOGICAL METHODS

Windshield splatter analysis with the Galaxy metagenomic pipeline

(2009) S. Kosakovsky Pond et al.   GENOME RESEARCH