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

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands

(2019) Joanna Warwick-Dugdale et al.   PeerJ

Optimizing de novo genome assembly from PCR-amplified metagenomes

(2019) Simon Roux et al.   PeerJ

High Initial Sputter Rate Found for Vaccinia Virions Using Isotopic Labeling, NanoSIMS, and AFM

(2018) Sean D. Gates et al.   ANALYTICAL CHEMISTRY

Quantifying aquatic viral community change associated with stormwater runoff in a wet retention pond using metagenomic time series data

(2018) JC Green et al.   AQUATIC MICROBIAL ECOLOGY

Diversity of DNA and RNA Viruses in Indoor Air As Assessed via Metagenomic Sequencing

(2018) Karyna Rosario et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The ‘Neglected’ Soil Virome – Potential Role and Impact

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

Exploring Viral Diversity in a Unique South African Soil Habitat

(2018) Jane Segobola et al.   Scientific Reports

Host-linked soil viral ecology along a permafrost thaw gradient

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

Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations

(2018) Timokratis Karamitros et al.   BMC GENOMICS

Genome-centric view of carbon processing in thawing permafrost

(2018) Ben J. Woodcroft et al.   NATURE

MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins

(2018) Deyvid Amgarten et al.   Frontiers in Genetics

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

(2018) Gareth Trubl et al.   mSystems

Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods

(2017) Alexis L. Pasulka et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient

(2017) Rhiannon Mondav et al.   ENVIRONMENTAL MICROBIOLOGY

Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data

(2017) David Paez-Espino et al.   Nature Protocols

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Chemical Composition of Soil Organic Matter in a Subarctic Peatland: Influence of Shifting Vegetation Communities

(2017) Anna E. Normand et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches

(2017) Stephen Hayes et al.   Viruses-Basel

Viral ecology comes of age

(2017) Matthew B. Sullivan et al.   Environmental Microbiology Reports

Soil Viral Communities Vary Temporally and along a Land Use Transect as Revealed by Virus-Like Particle Counting and a Modified Community Fingerprinting Approach (fRAPD)

(2017) Anja Narr et al.   Frontiers in Microbiology

The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis

(2017) Sylwia Zielińska et al.   MicrobiologyOpen

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

(2017) Simon Roux et al.   PeerJ

The Distribution, Evolution, and Roles of Gene Transfer Agents in Prokaryotic Genetic Exchange

(2017) Andrew S. Lang et al.   Annual Review of Virology

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

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

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

(2017) Jie Ren et al.   Microbiome

iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure

(2016) Benjamin Bolduc et al.   ISME Journal

Plankton networks driving carbon export in the oligotrophic ocean

(2016) Lionel Guidi et al.   NATURE

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

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

(2016) Simon Roux et al.   PeerJ

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

(2016) Christian Rinke et al.   PeerJ

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

(2016) Gareth Trubl et al.   PeerJ

Comparative assessment of methods for metagenomic DNA isolation from soils of different crop growing fields

(2016) Aiman Tanveer et al.   3 Biotech

An efficient and cost-effective method for DNA extraction from athalassohaline soil using a newly formulated cell extraction buffer

(2016) Avinash Narayan et al.   3 Biotech

Comparative assessment of methods for metagenomic DNA isolation from soils of different crop growing fields

(2016) Aiman Tanveer et al.   3 Biotech

An efficient and cost-effective method for DNA extraction from athalassohaline soil using a newly formulated cell extraction buffer

(2016) Avinash Narayan et al.   3 Biotech

Distinct Circular Single-Stranded DNA Viruses Exist in Different Soil Types

(2015) Brian Reavy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Diversity and Ecology of Viruses in Hyperarid Desert Soils

(2015) Olivier Zablocki et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The contentious nature of soil organic matter

(2015) Johannes Lehmann et al.   NATURE

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

Viral Transmission Dynamics at Single-Cell Resolution Reveal Transiently Immune Subpopulations Caused by a Carrier State Association

(2015) William Cenens et al.   PLoS Genetics

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Abstract 3564: A new method for preparation of low-input, PCR-free next generation sequencing libraries

(2015) Laurie Kurihara et al.   CANCER RESEARCH

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Development of a method to recovery and amplification DNA by real-time PCR from commercial vegetable oils

(2014) Sonia Ramos-Gómez et al.   FOOD CHEMISTRY

Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein

(2014) Max Hopkins et al.   ISME Journal

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

(2014) Li Deng et al.   NATURE

Methane dynamics regulated by microbial community response to permafrost thaw

(2014) Carmody K. McCalley et al.   NATURE

Changes in peat chemistry associated with permafrost thaw increase greenhouse gas production

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

Viruses as new agents of organomineralization in the geological record

(2014) Muriel Pacton et al.   Nature Communications

Discovery of a novel methanogen prevalent in thawing permafrost

(2014) Rhiannon Mondav et al.   Nature Communications

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

Sequencing platform and library preparation choices impact viral metagenomes

(2013) Sergei A Solonenko et al.   BMC GENOMICS

Evaluation of commercial kits for the extraction and purification of viral nucleic acids from environmental and fecal samples

(2013) Brandon C. Iker et al.   JOURNAL OF VIROLOGICAL METHODS

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

Environmental Monitoring and Research in the Abisko Area—An Overview

(2012) Christer Jonasson et al.   AMBIO

Net carbon accumulation of a high-latitude permafrost palsa mire similar to permafrost-free peatlands

(2012) David Olefeldt et al.   GEOPHYSICAL RESEARCH LETTERS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Fake virus particles generated by fluorescence microscopy

(2012) Patrick Forterre et al.   TRENDS IN MICROBIOLOGY

Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline

(2012) Melissa B. Duhaime et al.   VIROLOGY

VIROME: a standard operating procedure for analysis of viral metagenome sequences

(2012) K. Eric Wommack et al.   Standards in Genomic Sciences

Forensic implications of PCR inhibition—A review

(2011) Reza Alaeddini   Forensic Science International-Genetics

Accessing the Soil Metagenome for Studies of Microbial Diversity

(2010) Tom O. Delmont et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Detection of genetically modified soybean DNA in refined vegetable oils

(2010) Joana Costa et al.   EUROPEAN FOOD RESEARCH AND TECHNOLOGY

Multiple displacement amplification compromises quantitative analysis of metagenomes

(2010) Suzan Yilmaz et al.   NATURE METHODS

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

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

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

Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology

(2008) Erik K Binga et al.   ISME Journal