Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils
Published 2019 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils
Authors
Keywords
-
Journal
PeerJ
Volume 7, Issue -, Pages e7265
Publisher
PeerJ
Online
2019-07-04
DOI
10.7717/peerj.7265
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- 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
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started