Bacteriophages Roam the Wheat Phyllosphere

clinker & clustermap.js: automatic generation of gene cluster comparison figures

(2021) Cameron L M Gilchrist et al.   BIOINFORMATICS

Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter

(2021) Moïra B Dion et al.   NUCLEIC ACIDS RESEARCH

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

(2021) Jiarong Guo et al.   Microbiome

SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts

(2021) Ruoshi Zhang et al.   BIOINFORMATICS

Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay

(2021) Katrine Wacenius Skov Alanin et al.   Viruses-Basel

Metagenomics Analysis of the Wheat Virome Identifies Novel Plant and Fungal-Associated Viral Sequences

(2021) Carla Dizon Redila et al.   Viruses-Basel

Network Analysis of the Papaya Orchard Virome from Two Agroecological Regions of Chiapas, Mexico

(2020) Ricardo I. Alcalá-Briseño et al.   mSystems

The protector within: Comparative genomics of APSE phages across aphids reveals rampant recombination and diverse toxin arsenals

(2020) Jeff Rouïl et al.   Genome Biology and Evolution

A complex virome including two distinct emaraviruses associated with virus-like symptoms in Camellia japonica

(2020) C. Peracchio et al.   VIRUS RESEARCH

Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture

(2020) Jing Ke et al.   TRENDS IN BIOTECHNOLOGY

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

(2020) Kristopher Kieft et al.   Microbiome

The phyllosphere

(2020) Britt Koskella   CURRENT BIOLOGY

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

Systems Biology of Plant-Microbiome Interactions

(2019) Patricia A. Rodriguez et al.   Molecular Plant

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

Bacteriophages in Natural and Artificial Environments

(2019) Batinovic et al.   Pathogens

Pavian: Interactive analysis of metagenomics data for microbiome studies and pathogen identification

(2019) Florian P Breitwieser et al.   BIOINFORMATICS

Flag leaf size and posture of bread wheat: genetic dissection, QTL validation and their relationships with yield-related traits

(2019) Jian Ma et al.   THEORETICAL AND APPLIED GENETICS

A simple, reproducible and cost-effective procedure to analyse gut phageome: from phage isolation to bioinformatic approach

(2019) Camille d’Humières et al.   Scientific Reports

Gut Bacteriophage: Current Understanding and Challenges

(2019) Thomas D. S. Sutton et al.   Frontiers in Endocrinology

The impact of bacteriophages on phyllosphere bacterial abundance and composition

(2018) Norma M. Morella et al.   MOLECULAR ECOLOGY

Peach RNA viromes in six different peach cultivars

(2018) Yeonhwa Jo et al.   Scientific Reports

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

Virome analyses of Hevea brasiliensis using small RNA deep sequencing and PCR techniques reveal the presence of a potential new virus

(2018) Paula L. C. Fonseca et al.   Virology Journal

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Comparison of Microbial Communities Associated with Halophyte (Salsola stocksii) and Non-Halophyte (Triticum aestivum) Using Culture-Independent Approaches

(2017) Salma Mukhtar et al.   Polish Journal of Microbiology

Origins and challenges of viral dark matter

(2017) Siddharth R. Krishnamurthy et al.   VIRUS RESEARCH

Bacteriophage-Based Bacterial Wilt Biocontrol for an Environmentally Sustainable Agriculture

(2017) Belén Álvarez et al.   Frontiers in Plant Science

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

(2017) Simon Roux et al.   PeerJ

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Lytic to temperate switching of viral communities

(2016) B. Knowles et al.   NATURE

Ecogenomic survey of plant viruses infecting Tobacco by Next generation sequencing

(2016) Ibukun A. Akinyemi et al.   Virology Journal

Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer

(2016) Christian J. H. von Wintersdorff et al.   Frontiers in Microbiology

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

NCBI Viral Genomes Resource

(2014) J. Rodney Brister et al.   NUCLEIC ACIDS RESEARCH

Structure and Functions of the Bacterial Microbiota of Plants

(2013) Davide Bulgarelli et al.   Annual Review of Plant Biology

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Microbial life in the phyllosphere

(2012) Julia A. Vorholt   NATURE REVIEWS MICROBIOLOGY

Phage loss and the breakdown of a defensive symbiosis in aphids

(2012) S. R. Weldon et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Marine Viruses: Truth or Dare

(2011) Mya Breitbart   Annual Review of Marine Science

Biocontrol of Ralstonia solanacearum by Treatment with Lytic Bacteriophages

(2011) Akiko Fujiwara et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Amplification Methods Bias Metagenomic Libraries of Uncultured Single-Stranded and Double-Stranded DNA Viruses

(2011) Kyoung-Ho Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors

(2009) P. H. Degnan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Amplification of Uncultured Single-Stranded DNA Viruses from Rice Paddy Soil

(2008) K.-H. Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY