Diversities and potential biogeochemical impacts of mangrove soil viruses

The ‘Neglected’ Soil Virome – Potential Role and Impact

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

Metagenomics Investigation of Agarlytic Genes and Genomes in Mangrove Sediments in China: A Potential Repertory for Carbohydrate-Active Enzymes

(2018) Wu Qu et al.   Frontiers in Microbiology

Soil aggregates as massively concurrent evolutionary incubators

(2017) Matthias C Rillig et al.   ISME Journal

Marine microbiology: Algal virus boosts nitrogen uptake in the ocean

(2017) Ashley York   NATURE REVIEWS MICROBIOLOGY

Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions

(2017) Tianliang He et al.   mBio

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

Dietary energy drives the dynamic response of bovine rumen viral communities

(2017) Christopher L. Anderson et al.   Microbiome

Viral metabolic reprogramming in marine ecosystems

(2016) Bonnie L Hurwitz et al.   CURRENT OPINION IN MICROBIOLOGY

High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection

(2016) Jeroen De Smet et al.   ISME Journal

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Virocell Metabolism: Metabolic Innovations During Host–Virus Interactions in the Ocean

(2016) Shilo Rosenwasser et al.   TRENDS IN MICROBIOLOGY

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

(2016) Simon Roux et al.   PeerJ

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

(2015) Simon Roux et al.   ENVIRONMENTAL MICROBIOLOGY

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

Microbial hotspots and hot moments in soil: Concept & review

(2015) Yakov Kuzyakov et al.   SOIL BIOLOGY & BIOCHEMISTRY

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Carbon Cycling and Storage in Mangrove Forests

(2014) Daniel M. Alongi   Annual Review of Marine Science

Using Signature Genes as Tools To Assess Environmental Viral Ecology and Diversity

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

Metagenomic analysis of the viral community in Namib Desert hypoliths

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

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

(2014) S. N. Naccache et al.   GENOME RESEARCH

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

(2014) Bonnie L Hurwitz et al.   ISME Journal

The fate and biogeochemical cycling of viral elements

(2014) Rui Zhang et al.   NATURE REVIEWS MICROBIOLOGY

Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses

(2014) B. L. Hurwitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sulfur Oxidation Genes in Diverse Deep-Sea Viruses

(2014) K. Anantharaman et al.   SCIENCE

Environmental bacteriophages: viruses of microbes in aquatic ecosystems

(2014) Télesphore Sime-Ngando   Frontiers in Microbiology

Structure and function of a cyanophage-encoded peptide deformylase

(2013) Jeremy A Frank et al.   ISME Journal

Abundant SAR11 viruses in the ocean

(2013) Yanlin Zhao et al.   NATURE

Twelve previously unknown phage genera are ubiquitous in global oceans

(2013) K. Holmfeldt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

(2013) Simon Roux et al.   Nature Communications

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

(2013) S. Roux et al.   Open Biology

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

Marine Viruses Exploit Their Host's Two-Component Regulatory System in Response to Resource Limitation

(2012) Qinglu Zeng et al.   CURRENT BIOLOGY

Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method

(2012) Melissa B. Duhaime et al.   ENVIRONMENTAL MICROBIOLOGY

Complete Genome Sequence of Celeribacter Bacteriophage P12053L

(2012) I. Kang et al.   JOURNAL OF VIROLOGY

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics

(2012) Simon Roux et al.   PLoS One

The Microbiome of Brazilian Mangrove Sediments as Revealed by Metagenomics

(2012) Fernando Dini Andreote et al.   PLoS One

Carbon sequestration in mangrove forests

(2012) Daniel M Alongi   Carbon Management

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Marine Viruses: Truth or Dare

(2011) Mya Breitbart   Annual Review of Marine Science

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

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

Comparative metagenomics of microbial traits within oceanic viral communities

(2011) Itai Sharon et al.   ISME Journal

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

(2011) S. Powell et al.   NUCLEIC ACIDS RESEARCH

Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism

(2011) L. R. Thompson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Common origins and host-dependent diversity of plant and animal viromes

(2011) Valerian V Dolja et al.   Current Opinion in Virology

Reconstructing a puzzle: existence of cyanophages containing both photosystem-I and photosystem-II gene suites inferred from oceanic metagenomic datasets

(2010) Ariella Alperovitch-Lavy et al.   ENVIRONMENTAL MICROBIOLOGY

Diverse circovirus-like genome architectures revealed by environmental metagenomics

(2009) K. Rosario et al.   JOURNAL OF GENERAL VIROLOGY

Viruses manipulate the marine environment

(2009) Forest Rohwer et al.   NATURE

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes

(2008) H. Noguchi et al.   DNA RESEARCH

Exploring the diversity of bacterial communities in sediments of urban mangrove forests

(2008) Newton C. Marcial Gomes et al.   FEMS MICROBIOLOGY ECOLOGY

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE