DNase Treatment Improves Viral Enrichment in Agricultural Soil Viromes

Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities

(2021) Christian Santos-Medellin et al.   ISME Journal

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

(2021) Jiarong Guo et al.   Microbiome

A Roadmap for Genome-Based Phage Taxonomy

(2021) Dann Turner et al.   Viruses-Basel

Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities

(2021) Alexa M. Nicolas et al.   mSystems

Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities

(2020) Paul Carini et al.   mBio

Uncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil

(2020) Pauline C. Göller et al.   Microbiome

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 Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut

(2020) Ann C. Gregory et al.   Cell Host & Microbe

Evaluation of DESS as a storage medium for microbial community analysis

(2019) Kevin M. Lee et al.   PeerJ

Viability of Bacillus subtilis (natto) Bacteriophages after Freezing and Thawing

(2019) Toshirou NAGAI   JARQ-JAPAN AGRICULTURAL RESEARCH QUARTERLY

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

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

Soil Viruses: A New Hope

(2019) Joanne B. Emerson   mSystems

Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils

(2019) Gareth Trubl et al.   PeerJ

Implication of Viral Infections for Greenhouse Gas Dynamics in Freshwater Wetlands: Challenges and Perspectives

(2019) Giuditta Bonetti et al.   Frontiers in Microbiology

Phage combination therapies for bacterial wilt disease in tomato

(2019) Xiaofang Wang et al.   NATURE BIOTECHNOLOGY

The ‘Neglected’ Soil Virome – Potential Role and Impact

(2018) Akbar Adjie Pratama et al.   TRENDS IN MICROBIOLOGY

How, When, and Where Relic DNA Affects Microbial Diversity

(2018) J. T. Lennon et al.   mBio

Host-linked soil viral ecology along a permafrost thaw gradient

(2018) Joanne B. Emerson et al.   Nature Microbiology

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

Viruses in soil: Nano-scale undead drivers of microbial life, biogeochemical turnover and ecosystem functions

(2018) Yakov Kuzyakov et al.   SOIL BIOLOGY & BIOCHEMISTRY

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

(2018) Gareth Trubl et al.   mSystems

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

(2017) Benjamin Bolduc et al.   PeerJ

Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory

(2017) Kurt E. Williamson et al.   Annual Review of Virology

Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems

(2017) Joanne B. Emerson et al.   Microbiome

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient

(2016) Gareth Trubl et al.   PeerJ

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

(2016) Paul Carini et al.   Nature Microbiology

Integrity of the Human Faecal Microbiota following Long-Term Sample Storage

(2016) Elahe Kia et al.   PLoS One

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

(2015) Tal Galili   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Rising to the challenge: accelerated pace of discovery transforms marine virology

(2015) Jennifer R. Brum et al.   NATURE REVIEWS MICROBIOLOGY

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

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

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences

(2013) S. Roux et al.   Open Biology

Dynamic Viral Populations in Hypersaline Systems as Revealed by Metagenomic Assembly

(2012) Joanne B. Emerson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Characterization of the Fecal Microbiota Using High-Throughput Sequencing Reveals a Stable Microbial Community during Storage

(2012) Ian M. Carroll et al.   PLoS One

Marine Viruses: Truth or Dare

(2011) Mya Breitbart   Annual Review of Marine Science

The influence of external factors on bacteriophages—review

(2011) E. Jończyk et al.   FOLIA MICROBIOLOGICA

High frequency of phage-infected bacterial cells in a rice field soil in Japan

(2011) Ryu Takahashi et al.   SOIL SCIENCE AND PLANT NUTRITION

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Viral and microbial community dynamics in four aquatic environments

(2010) Beltran Rodriguez-Brito et al.   ISME Journal

High frequency of virus-infected bacterial cells in a sheep grazed pasture soil in New Zealand

(2010) Saman Bowatte et al.   SOIL BIOLOGY & BIOCHEMISTRY

Ecology of viruses in soils: Past, present and future perspectives

(2010) Makoto Kimura et al.   SOIL SCIENCE AND PLANT NUTRITION

A simple and efficient method for concentration of ocean viruses by chemical flocculation

(2010) Seth G. John et al.   Environmental Microbiology Reports

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

Assembly of Viral Metagenomes from Yellowstone Hot Springs

(2008) T. Schoenfeld et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY