Putative archaeal viruses from the mesopelagic ocean

Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean

(2017) Yosuke Nishimura et al.   mSphere

Viruses Inhibit CO 2 Fixation in the Most Abundant Phototrophs on Earth

(2016) Richard J. Puxty et al.   CURRENT BIOLOGY

Viral metabolic reprogramming in marine ecosystems

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

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

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

Viral interference of the bacterial RNA metabolism machinery

(2016) Tom Dendooven et al.   RNA Biology

Virus-mediated archaeal hecatomb in the deep seafloor

(2016) R. Danovaro et al.   Science Advances

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

(2015) Jessica M Labonté et al.   ISME Journal

Tritagonist as a new term for uncharacterised microorganisms in environmental systems

(2015) Florian M Freimoser et al.   ISME Journal

Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone

(2015) Sangita Ganesh et al.   ISME Journal

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

Targeted diversity generation by intraterrestrial archaea and archaeal viruses

(2015) Blair G. Paul et al.   Nature Communications

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

(2015) Simon Roux et al.   eLife

Marine Group II Archaea, potentially important players in the global ocean carbon cycle

(2015) Chuanlun L. Zhang et al.   Frontiers in Microbiology

Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions

(2015) Cheryl-Emiliane T. Chow et al.   Frontiers in Microbiology

Standard filtration practices may significantly distort planktonic microbial diversity estimates

(2015) Cory C. Padilla et al.   Frontiers in Microbiology

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Aerobic Microbial Respiration In Oceanic Oxygen Minimum Zones

(2015) Tim Kalvelage et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Metavir 2: new tools for viral metagenome comparison and assembled virome analysis

(2014) Simon Roux et al.   BMC BIOINFORMATICS

A New Highly Sensitive Method to Assess Respiration Rates and Kinetics of Natural Planktonic Communities by Use of the Switchable Trace Oxygen Sensor and Reduced Oxygen Concentrations

(2014) Laura Tiano et al.   PLoS One

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes

(2014) A. K. Hawley 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

BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees

(2014) Daniel L. Rabosky et al.   Methods in Ecology and Evolution

Archaeal Viruses: Diversity, Replication, and Structure

(2014) Nikki Dellas et al.   Annual Review of Virology

Living Side by Side with a Virus: Characterization of Two Novel Plasmids from Thermococcus prieurii, a Host for the Spindle-Shaped Virus TPV1

(2013) Aurore Gorlas et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

New Approaches Indicate Constant Viral Diversity despite Shifts in Assemblage Structure in an Australian Hypersaline Lake

(2013) Joanne B. Emerson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses

(2013) Elke Allers et al.   ENVIRONMENTAL MICROBIOLOGY

Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition

(2013) Nana Yaw D Ankrah et al.   ISME Journal

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Microbial community structure and productivity in the oxygen minimum zone of the eastern tropical North Pacific

(2012) Agnieszka Podlaska et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Phylogenomics of T4 cyanophages: lateral gene transfer in the ‘core’ and origins of host genes

(2012) J. Cesar Ignacio-Espinoza et al.   ENVIRONMENTAL MICROBIOLOGY

Oxygen minimum zones harbour novel viral communities with low diversity

(2012) Noriko Cassman et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean

(2012) Elke Allers et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Microbial ecology of expanding oxygen minimum zones

(2012) Jody J. Wright et al.   NATURE REVIEWS MICROBIOLOGY

Microbial oceanography of anoxic oxygen minimum zones

(2012) O. Ulloa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

(2012) V. Iverson et al.   SCIENCE

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

TPV1, the first virus isolated from the hyperthermophilic genus Thermococcus

(2011) Aurore Gorlas et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial metatranscriptomics in a permanent marine oxygen minimum zone

(2011) Frank J. Stewart et al.   ENVIRONMENTAL MICROBIOLOGY

Abundance and phylogenetic identity of archaeoplankton in the permanent oxygen minimum zone of the eastern tropical South Pacific

(2011) Lucy Belmar et al.   FEMS MICROBIOLOGY ECOLOGY

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

Microbial Nitrogen Cycling Processes in Oxygen Minimum Zones

(2010) Phyllis Lam et al.   Annual Review of Marine Science

The phage-host arms race: Shaping the evolution of microbes

(2010) Adi Stern et al.   BIOESSAYS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Tonicity-responsive microRNAs contribute to the maximal induction of osmoregulatory transcription factor OREBP in response to high-NaCl hypertonicity

(2010) Weifeng Huang et al.   NUCLEIC ACIDS RESEARCH

Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins

(2010) Nicolas Soler et al.   NUCLEIC ACIDS RESEARCH

Early Evolution of Photosynthesis

(2010) R. E. Blankenship   PLANT PHYSIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Evolution and Future of Earth’s Nitrogen Cycle

(2010) Donald E. Canfield et al.   SCIENCE

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Local Adaptation of Bacteriophages to Their Bacterial Hosts in Soil

(2009) M. Vos et al.   SCIENCE

Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea

(2009) Yvan Zivanovic et al.   GENOME BIOLOGY

Bacterial diversity in the oxygen minimum zone of the eastern tropical South Pacific

(2008) Heike Stevens et al.   ENVIRONMENTAL MICROBIOLOGY

Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

(2008) G. Lima-Mendez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evidence for the Intense Exchange of MazG in Marine Cyanophages by Horizontal Gene Transfer

(2008) Michael J. Bryan et al.   PLoS One