Diversity and potential biogeochemical impacts of viruses in bulk and rhizosphere soils

Soil microbial diversity drops with land‐use change in a high mountain temperate forest: a metagenomics survey

(2020) Ligia C. Muñoz‐Arenas et al.   Environmental Microbiology Reports

Bioarchaeology: a profitable dialogue between microbiology and archaeology

(2020) Harald Brüssow   Microbial Biotechnology

Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils

(2019) Zhi-Bo Zhao et al.   Microbiome

A specialized metabolic network selectively modulates Arabidopsis root microbiota

(2019) Ancheng C. Huang et al.   SCIENCE

Rhizosphere size and shape: Temporal dynamics and spatial stationarity

(2019) Yakov Kuzyakov et al.   SOIL BIOLOGY & BIOCHEMISTRY

Diversities and potential biogeochemical impacts of mangrove soil viruses

(2019) Min Jin et al.   Microbiome

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

Characterization of Rhodopseudomonas palustris population dynamics on tobacco phyllosphere and induction of plant resistance to Tobacco mosaic virus

(2019) Pin Su et al.   Microbial Biotechnology

Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

(2019) Evan P. Starr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Viral abundance and diversity vary with depth in a southeastern United States agricultural ultisol

(2019) Xiaolong Liang et al.   SOIL BIOLOGY & BIOCHEMISTRY

Phage combination therapies for bacterial wilt disease in tomato

(2019) Xiaofang Wang et al.   NATURE BIOTECHNOLOGY

OUP accepted manuscript

(2018)   BIOINFORMATICS

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Host-linked soil viral ecology along a permafrost thaw gradient

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

Host range and molecular characterization of a lytic Pradovirus-like Ralstonia phage RsoP1IDN isolated from Indonesia

(2018) Hardian Susilo Addy et al.   ARCHIVES OF VIROLOGY

Viral and metabolic controls on high rates of microbial sulfur and carbon cycling in wetland ecosystems

(2018) Paula Dalcin Martins et al.   Microbiome

Unraveling Microbial Communities Associated with Methylmercury Production in Paddy Soils

(2018) Yu-Rong Liu et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

Hidden diversity of soil giant viruses

(2018) Frederik Schulz et al.   Nature Communications

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

(2018) Gareth Trubl et al.   mSystems

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Diversity and Distribution Characteristics of Viruses in Soils of a Marine-Terrestrial Ecotone in East China

(2017) Dan-Ting Yu et al.   MICROBIAL ECOLOGY

Rhizosphere-associated bacterial network structure and spatial distribution differ significantly from bulk soil in wheat crop fields

(2017) Kunkun Fan et al.   SOIL BIOLOGY & BIOCHEMISTRY

Marine Viruses: Key Players in Marine Ecosystems

(2017) Mathias Middelboe et al.   Viruses-Basel

Genetic and functional diversity of ubiquitous DNA viruses in selected Chinese agricultural soils

(2017) Li-Li Han et al.   Scientific Reports

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

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

Environmental drivers of viral community composition in Antarctic soils identified by viromics

(2017) Evelien M. Adriaenssens et al.   Microbiome

Dietary energy drives the dynamic response of bovine rumen viral communities

(2017) Christopher L. Anderson et al.   Microbiome

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees

(2016) Zilong He et al.   NUCLEIC ACIDS RESEARCH

Towards quantitative viromics for both double-stranded and single-stranded DNA viruses

(2016) Simon Roux et al.   PeerJ

Viruses as Winners in the Game of Life

(2016) Ana Georgina Cobián Güemes et al.   Annual Review of Virology

Analysis of metagenomic data reveals common features of halophilic viral communities across continents

(2015) Simon Roux et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Database resources of the National Center for Biotechnology Information

(2015)   NUCLEIC ACIDS RESEARCH

Impacts of bulk soil microbial community structure on rhizosphere microbiomes of Zea mays

(2015) Matthew G. Bakker et al.   PLANT AND SOIL

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Metagenomic analysis of the viral community in Namib Desert hypoliths

(2014) Evelien M. Adriaenssens et al.   ENVIRONMENTAL MICROBIOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome

(2014) Rachel Marine et al.   Microbiome

PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: What null hypothesis are you testing?

(2013) Marti J. Anderson et al.   ECOLOGICAL MONOGRAPHS

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology

(2013) Bonnie L. Hurwitz et al.   PLoS One

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

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Going viral: next-generation sequencing applied to phage populations in the human gut

(2012) Alejandro Reyes et al.   NATURE REVIEWS 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

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

ggplot2: Elegant Graphics for Data Analysis

(2011) Cedric Ginestet   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES A-STATISTICS IN SOCIETY

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Global regulation by the seven-component Pi signaling system

(2010) Yi-Ju Hsieh et al.   CURRENT OPINION IN MICROBIOLOGY

Viruses manipulate the marine environment

(2009) Forest Rohwer et al.   NATURE

Impact of wheat straw decomposition on successional patterns of soil microbial community structure

(2008) Fabiola Bastian et al.   SOIL BIOLOGY & BIOCHEMISTRY