Related references
Note: Only part of the references are listed.The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project
David J. Weston et al.
NEW PHYTOLOGIST (2018)
Using Metagenomics to Characterize an Expanding Virosphere
Yong-Zhen Zhang et al.
CELL (2018)
The soil microbiome - from metagenomics to metaphenomics
Janet K. Jansson et al.
CURRENT OPINION IN MICROBIOLOGY (2018)
Biological species in the viral world
Louis-Marie Bobay et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
A global atlas of the dominant bacteria found in soil
Manuel Delgado-Baquerizo et al.
SCIENCE (2018)
The 'Neglected' Soil Virome - Potential Role and Impact
Akbar Adjie Pratama et al.
TRENDS IN MICROBIOLOGY (2018)
Bioreactor virome metagenomics sequencing using DNA spike-ins
Geert Cremers et al.
PEERJ (2018)
Host-linked soil viral ecology along a permafrost thaw gradient
Joanne B. Emerson et al.
NATURE MICROBIOLOGY (2018)
Genome-centric view of carbon processing in thawing permafrost
Ben J. Woodcroft et al.
NATURE (2018)
Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios
Heli Juottonen et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2017)
Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper-arid polar desert
Jacqueline Goordial et al.
ENVIRONMENTAL MICROBIOLOGY (2017)
iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure
Benjamin Bolduc et al.
ISME JOURNAL (2017)
Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient
Rhiannon Mondav et al.
ENVIRONMENTAL MICROBIOLOGY (2017)
Large uncertainty in permafrost carbon stocks due to hillslope soil deposits
Eitan Shelef et al.
GEOPHYSICAL RESEARCH LETTERS (2017)
Embracing the unknown: disentangling the complexities of the soil microbiome
Noah Fierer
NATURE REVIEWS MICROBIOLOGY (2017)
Hydrogenation of organic matter as a terminal electron sink sustains high CO2:CH4 production ratios during anaerobic decomposition
Rachel M. Wilson et al.
ORGANIC GEOCHEMISTRY (2017)
Chemical Composition of Soil Organic Matter in a Subarctic Peatland: Influence of Shifting Vegetation Communities
Anna E. Normand et al.
SOIL SCIENCE SOCIETY OF AMERICA JOURNAL (2017)
Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches
Stephen Hayes et al.
VIRUSES-BASEL (2017)
Marine Viruses: Key Players in Marine Ecosystems
Mathias Middelboe et al.
VIRUSES-BASEL (2017)
Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling
Jia Deng et al.
JOURNAL OF ADVANCES IN MODELING EARTH SYSTEMS (2017)
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)
Anja Narr et al.
FRONTIERS IN MICROBIOLOGY (2017)
Putative archaeal viruses from the mesopelagic ocean
Dean R. Vik et al.
PEERJ (2017)
vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria
Benjamin Bolduc et al.
PEERJ (2017)
Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
Simon Roux et al.
PEERJ (2017)
The Distribution, Evolution, and Roles of Gene Transfer Agents in Prokaryotic Genetic Exchange
Andrew S. Lang et al.
Annual Review of Virology (2017)
Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory
Kurt E. Williamson et al.
ANNUAL REVIEW OF VIROLOGY, VOL 4 (2017)
Environmental drivers of viral community composition in Antarctic soils identified by viromics
Evelien M. Adriaenssens et al.
MICROBIOME (2017)
Dietary energy drives the dynamic response of bovine rumen viral communities
Christopher L. Anderson et al.
MICROBIOME (2017)
Greenhouse gas balance over thaw-freeze cycles in discontinuous zone permafrost
R. M. Wilson et al.
JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES (2017)
A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells
Svetlana Fridman et al.
NATURE MICROBIOLOGY (2017)
Diversity and Ecology of Viruses in Hyperarid Desert Soils
Olivier Zablocki et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2016)
Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics
Jennifer R. Brum et al.
ISME JOURNAL (2016)
Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer
Ann C. Gregory et al.
BMC GENOMICS (2016)
The bright side of microbial dark matter: lessons learned from the uncultivated majority
Lindsey Solden et al.
CURRENT OPINION IN MICROBIOLOGY (2016)
Methanogenic paraffin degradation proceeds via alkane addition to fumarate by Smithella' spp. mediated by a syntrophic coupling with hydrogenotrophic methanogens
Boris Wawrik et al.
ENVIRONMENTAL MICROBIOLOGY (2016)
Seascapes as a new vernacular for pelagic ocean monitoring, management and conservation
Maria T. Kavanaugh et al.
ICES JOURNAL OF MARINE SCIENCE (2016)
Peat: home to novel syntrophic species that feed acetate- and hydrogen-scavenging methanogens
Oliver Schmidt et al.
ISME JOURNAL (2016)
Plankton networks driving carbon export in the oligotrophic ocean
Lionel Guidi et al.
NATURE (2016)
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses
Simon Roux et al.
NATURE (2016)
The genomic content and context of auxiliary metabolic genes in marine cyanomyoviruses
Lisa T. Crummett et al.
VIROLOGY (2016)
Potential carbon emissions dominated by carbon dioxide from thawed permafrost soils
Christina Schadel et al.
NATURE CLIMATE CHANGE (2016)
Characterization of Noval Bacteriophages for Biocontrol of Bacterial Blight in Leek Caused by Pseudomonas syringae pv. porri
Sofie Rombouts et al.
FRONTIERS IN MICROBIOLOGY (2016)
The Ecology of Acidobacteria: Moving beyond Genes and Genomes
Anna M. Kielak et al.
FRONTIERS IN MICROBIOLOGY (2016)
Towards quantitative viromics for both double-stranded and single-stranded DNA viruses
Simon Roux et al.
PEERJ (2016)
Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics
Christian Rinke et al.
PEERJ (2016)
Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient
Gareth Trubl et al.
PEERJ (2016)
Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales
Rebecca A. Daly et al.
NATURE MICROBIOLOGY (2016)
Computational approaches to predict bacteriophage-host relationships
Robert A. Edwards et al.
FEMS MICROBIOLOGY REVIEWS (2016)
Dark Matter of the Biosphere: the Amazing World of Bacteriophage Diversity
Graham F. Hatfull
JOURNAL OF VIROLOGY (2015)
Climate change and the permafrost carbon feedback
E. A. G. Schuur et al.
NATURE (2015)
The I-TASSER Suite: protein structure and function prediction
Jianyi Yang et al.
NATURE METHODS (2015)
Rising to the challenge: accelerated pace of discovery transforms marine virology
Jennifer R. Brum et al.
NATURE REVIEWS MICROBIOLOGY (2015)
Patterns and ecological drivers of ocean viral communities
Jennifer R. Brum et al.
SCIENCE (2015)
Diverse uncultivated ultra-small bacterial cells in groundwater
Birgit Luef et al.
NATURE COMMUNICATIONS (2015)
Viral dark matter and virus-host interactions resolved from publicly available microbial genomes
Simon Roux et al.
ELIFE (2015)
Peripheral Blood Mononuclear Cell Gene Expression Remains Broadly Altered Years after Successful Interferon-Based Hepatitis C Virus Treatment
Paul Ravi Waldron et al.
JOURNAL OF IMMUNOLOGY RESEARCH (2015)
VirSorter: mining viral signal from microbial genomic data
Simon Roux et al.
PEERJ (2015)
Depth-stratified functional and taxonomic niche specialization in the 'core' and 'flexible' Pacific Ocean Virome
Bonnie L. Hurwitz et al.
ISME JOURNAL (2015)
NCBI Viral Genomes Resource
J. Rodney Brister et al.
NUCLEIC ACIDS RESEARCH (2015)
Comparative Genomics of Cluster O Mycobacteriophages
Steven G. Cresawn et al.
PLOS ONE (2015)
Linking environmental prokaryotic viruses and their host through CRISPRs
Laura Sanguino et al.
FEMS MICROBIOLOGY ECOLOGY (2015)
High-Level Diversity of Tailed Phages, Eukaryote-Associated Viruses, and Virophage-Like Elements in the Metaviromes of Antarctic Soils
Olivier Zablocki et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2014)
Brine Assemblages of Ultrasmall Microbial Cells within the Ice Cover of Lake Vida, Antarctica
Emanuele Kuhn et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2014)
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M. Bolger et al.
BIOINFORMATICS (2014)
Determinants of Acidobacteria activity inferred from the relative abundances of 16S rRNA transcripts in German grassland and forest soils
Baerbel U. Foesel et al.
ENVIRONMENTAL MICROBIOLOGY (2014)
Methane dynamics regulated by microbial community response to permafrost thaw
Carmody K. McCalley et al.
NATURE (2014)
The microbial ecology of permafrost
Janet K. Jansson et al.
NATURE REVIEWS MICROBIOLOGY (2014)
Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses
Bonnie L. Hurwitz et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Changes in peat chemistry associated with permafrost thaw increase greenhouse gas production
Suzanne B. Hodgkins et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Sulfur Oxidation Genes in Diverse Deep-Sea Viruses
Karthik Anantharaman et al.
SCIENCE (2014)
Discovery of a novel methanogen prevalent in thawing permafrost
Rhiannon Mondav et al.
NATURE COMMUNICATIONS (2014)
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
Paul J. McMurdie et al.
PLOS COMPUTATIONAL BIOLOGY (2014)
Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome
Rachel Marine et al.
MICROBIOME (2014)
Estimates of viral abundance in soils are strongly influenced by extraction and enumeration methods
Kurt E. Williamson et al.
BIOLOGY AND FERTILITY OF SOILS (2013)
Are we missing half of the viruses in the ocean?
Grieg F. Steward et al.
ISME JOURNAL (2013)
To kill or not to kill: The balance between lytic and lysogenic viral infection is driven by trophic status
Jerome P. Payet et al.
LIMNOLOGY AND OCEANOGRAPHY (2013)
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Christian Quast et al.
NUCLEIC ACIDS RESEARCH (2013)
Crass: identification and reconstruction of CRISPR from unassembled metagenomic data
Connor T. Skennerton et al.
NUCLEIC ACIDS RESEARCH (2013)
Long-term CO2 production following permafrost thaw
Bo Elberling et al.
NATURE CLIMATE CHANGE (2013)
Metabolic reprogramming by viruses in the sunlit and dark ocean
Bonnie L. Hurwitz et al.
GENOME BIOLOGY (2013)
Monitoring the Multi-Year Carbon Balance of a Subarctic Palsa Mire with Micrometeorological Techniques
Torben R. Christensen et al.
AMBIO (2012)
Marine Viruses: Truth or Dare
Mya Breitbart
ANNUAL REVIEW OF MARINE SCIENCE, VOL 4 (2012)
Regional Variation in Lytic and Lysogenic Viral Infection in the Southern Ocean and Its Contribution to Biogeochemical Cycling
Claire Evans et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2012)
Gene and translation initiation site prediction in metagenomic sequences
Doug Hyatt et al.
BIOINFORMATICS (2012)
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
Yu Peng et al.
BIOINFORMATICS (2012)
Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method
Melissa B. Duhaime et al.
ENVIRONMENTAL MICROBIOLOGY (2012)
Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers
Martina Stursova et al.
FEMS MICROBIOLOGY ECOLOGY (2012)
Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches
Ramiro Logares et al.
JOURNAL OF MICROBIOLOGICAL METHODS (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
Cellulolytic bacteria from soils in harsh environments
Fabio Lino Soares et al.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY (2012)
High Resolution Mapping of Peatland Hydroperiod at a High-Latitude Swedish Mire
Nathan Torbick et al.
REMOTE SENSING (2012)
Metagenomic analysis of a southern maritime Antarctic
David A. Pearce et al.
FRONTIERS IN MICROBIOLOGY (2012)
Unraveling the viral tapestry (from inside the capsid out)
Shawn W. Polson et al.
ISME JOURNAL (2011)
Comparative metagenomics of microbial traits within oceanic viral communities
Itai Sharon et al.
ISME JOURNAL (2011)
Genome Sequence of Pedosphaera parvula Ellin514, an Aerobic Verrucomicrobial Isolate from Pasture Soil
Ravi Kant et al.
JOURNAL OF BACTERIOLOGY (2011)
The under-recognized dominance of Verrucomicrobia in soil bacterial communities
Gaddy T. Bergmann et al.
SOIL BIOLOGY & BIOCHEMISTRY (2011)
Pattern Recognition Receptors and the Innate Immune Response to Viral Infection
Mikayla R. Thompson et al.
VIRUSES-BASEL (2011)
A simple and efficient method for concentration of ocean viruses by chemical flocculation
Seth G. John et al.
ENVIRONMENTAL MICROBIOLOGY REPORTS (2011)
Exploring the viral world through metagenomics
Karyna Rosario et al.
CURRENT OPINION IN VIROLOGY (2011)
Search and clustering orders of magnitude faster than BLAST
Robert C. Edgar
BIOINFORMATICS (2010)
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments
Alexis Criscuolo et al.
BMC EVOLUTIONARY BIOLOGY (2010)
Insights into the function of the WhiB-like protein of mycobacteriophage TM4-a transcriptional inhibitor of WhiB2
Jan Rybniker et al.
MOLECULAR MICROBIOLOGY (2010)
Multiple displacement amplification compromises quantitative analysis of metagenomes
Suzan Yilmaz et al.
NATURE METHODS (2010)
Network analyses structure genetic diversity in independent genetic worlds
Sebastien Halary et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Soil organic carbon pools in the northern circumpolar permafrost region
C. Tarnocai et al.
GLOBAL BIOGEOCHEMICAL CYCLES (2009)
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
Morgan N. Price et al.
MOLECULAR BIOLOGY AND EVOLUTION (2009)
Laboratory procedures to generate viral metagenomes
Rebecca V. Thurber et al.
NATURE PROTOCOLS (2009)
Improved Attribution of Climate Forcing to Emissions
Drew T. Shindell et al.
SCIENCE (2009)
Linking habitat modification to catastrophic shifts and vegetation patterns in bogs
Maarten B. Eppinga et al.
PLANT ECOLOGY (2009)
Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology
Erik K. Binga et al.
ISME JOURNAL (2008)
Reticulate representation of evolutionary and functional relationships between phage genomes
Gipsi Lima-Mendez et al.
MOLECULAR BIOLOGY AND EVOLUTION (2008)
Functional metagenomic profiling of nine biomes
Elizabeth A. Dinsdale et al.
NATURE (2008)
Phages across the biosphere: contrasts of viruses in soil and aquatic environments
Sharath Srinivasiah et al.
RESEARCH IN MICROBIOLOGY (2008)
Ecology of viruses in soils: Past, present and future perspectives
Makoto Kimura et al.
SOIL SCIENCE AND PLANT NUTRITION (2008)
Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil
Noah Fierer et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)
Marine viruses - major players in the global ecosystem
Curtis A. Suttle
NATURE REVIEWS MICROBIOLOGY (2007)
Toward an ecological classification of soil bacteria
Noah Fierer et al.
ECOLOGY (2007)
Viral dynamics and patterns of lysogeny in saline Antarctic lakes
Johanna Laybourn-Parry et al.
POLAR BIOLOGY (2007)
The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families
Shibu Yooseph et al.
PLOS BIOLOGY (2007)
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
Ivica Letunic et al.
BIOINFORMATICS (2007)
Vegetation, climatic changes and net carbon sequestration in a North-Scandinavian subarctic mire over 30 years
N Malmer et al.
GLOBAL CHANGE BIOLOGY (2005)
InterProScan: protein domains identifier
E Quevillon et al.
NUCLEIC ACIDS RESEARCH (2005)
Captured diversity in a culture collection: Case study of the geographic and habitat distributions of environmental isolates held at the American type culture collection
MM Floyd et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2005)
TM-align: a protein structure alignment algorithm based on the TM-score
Y Zhang et al.
NUCLEIC ACIDS RESEARCH (2005)
MUSCLE: multiple sequence alignment with high accuracy and high throughput
RC Edgar
NUCLEIC ACIDS RESEARCH (2004)
Thawing sub-arctic permafrost:: Effects on vegetation and methane emissions -: art. no. L04501
TR Christensen et al.
GEOPHYSICAL RESEARCH LETTERS (2004)
Phage-host interaction:: an ecological perspective
S Chibani-Chennoufi et al.
JOURNAL OF BACTERIOLOGY (2004)
Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics
A Quaiser et al.
MOLECULAR MICROBIOLOGY (2003)
Viruses from extreme thermal environments
G Rice et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
KEGG: Kyoto Encyclopedia of Genes and Genomes
M Kanehisa et al.
NUCLEIC ACIDS RESEARCH (2000)
Share Paper
