Cyanophage host‐derived genes reflect contrasting selective pressures with depth in the oxic and anoxic water column of the Eastern Tropical North Pacific

Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column

(2020) Elaine Luo et al.   ISME Journal

Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments

(2020) Asier Zaragoza-Solas et al.   mSystems

Co-culture and biogeography of Prochlorococcus and SAR11

(2019) Jamie W. Becker et al.   ISME Journal

Different ways of doing the same: variations in the two last steps of the purine biosynthetic pathway in prokaryotes

(2019) Dennifier Costa Brandão Cruz et al.   Genome Biology and Evolution

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

Complete arsenic-based respiratory cycle in the marine microbial communities of pelagic oxygen-deficient zones

(2019) Jaclyn K. Saunders et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A novel uncultured marine cyanophage lineage with lysogenic potential linked to a putative marine Synechococcus ‘relic’ prophage

(2019) José Flores‐Uribe et al.   Environmental Microbiology Reports

Cyanobacteria and cyanophage contributions to carbon and nitrogen cycling in an oligotrophic oxygen-deficient zone

(2019) Clara A. Fuchsman et al.   ISME Journal

Cyanobacterial viruses exhibit diurnal rhythms during infection

(2019) Riyue Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nitrogen sourcing during viral infection of marine cyanobacteria

(2019) Jacob R. Waldbauer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Energy limitation of cyanophage development: implications for marine carbon cycling

(2018) Richard J. Puxty et al.   ISME Journal

Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

(2018) F. Lemoine et al.   NATURE

Marine microbial metagenomes sampled across space and time

(2018) Steven J. Biller et al.   Scientific Data

Transcriptomic responses of the marine cyanobacterium Prochlorococcus to viral lysis products

(2018) Xiaoting Fang et al.   ENVIRONMENTAL MICROBIOLOGY

Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes

(2018) Nathan A. Ahlgren et al.   ISME Journal

Lateral Gene Transfer Shapes the Distribution of RuBisCO among Candidate Phyla Radiation Bacteria and DPANN Archaea

(2018) Alexander L Jaffe et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cyanophage-encoded lipid desaturases: oceanic distribution, diversity and function

(2017) Sheila Roitman et al.   ISME Journal

Energetic cost of building a virus

(2017) Gita Mahmoudabadi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cryptic oxygen cycling in anoxic marine zones

(2017) Emilio Garcia-Robledo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone

(2017) Clara A. Fuchsman et al.   Frontiers in Microbiology

Putative archaeal viruses from the mesopelagic ocean

(2017) Dean R. Vik et al.   PeerJ

Quantification of diverse virus populations in the environment using the polony method

(2017) Nava Baran et al.   Nature Microbiology

A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells

(2017) Svetlana Fridman et al.   Nature Microbiology

Effect of the oxygen minimum zone on the second chlorophyll maximum

(2017) J Cepeda-Morales   CIENCIAS MARINAS

Genomic diversification of marine cyanophages into stable ecotypes

(2016) Marcia F. Marston et al.   ENVIRONMENTAL MICROBIOLOGY

The genomic content and context of auxiliary metabolic genes in marine cyanomyoviruses

(2016) Lisa T. Crummett et al.   VIROLOGY

The Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing

(2016) Jaime Iranzo et al.   mBio

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages

(2015) C Chénard et al.   ISME Journal

Genomic potential for arsenic efflux and methylation varies among global Prochlorococcus populations

(2015) Jaclyn K Saunders et al.   ISME Journal

Transcriptome dynamics of a broad host-range cyanophage and its hosts

(2015) Shany Doron et al.   ISME Journal

Spontaneous Deletion of an “ORFanage” Region Facilitates Host Adaptation in a “Photosynthetic” Cyanophage

(2015) Richard J. Puxty et al.   PLoS One

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Marine Cyanophages Demonstrate Biogeographic Patterns throughout the Global Ocean

(2014) Sijun Huang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Oxygen distribution and aerobic respiration in the north and south eastern tropical Pacific oxygen minimum zones

(2014) Laura Tiano et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

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

(2014) Bonnie L Hurwitz et al.   ISME Journal

Effect of P-limitation on prokaryotic and viral production in surface waters of the Northwestern Mediterranean Sea

(2014) Chiaki Motegi et al.   JOURNAL OF PLANKTON RESEARCH

The effect of organic carbon on fixed nitrogen loss in the eastern tropical South Pacific and Arabian Sea oxygen deficient zones

(2014) Bonnie X. Chang et al.   LIMNOLOGY AND OCEANOGRAPHY

Organic Matter Stoichiometry, Flux, and Oxygen Control Nitrogen Loss in the Ocean

(2014) A. R. Babbin et al.   SCIENCE

Comparative metagenomic analyses reveal viral-induced shifts of host metabolism towards nucleotide biosynthesis

(2014) Hagay Enav et al.   Microbiome

The purinosome, a multi-protein complex involved in the de novo biosynthesis of purines in humans

(2013) Hong Zhao et al.   CHEMICAL COMMUNICATIONS

Diversity and evolutionary relationships of T7-like podoviruses infecting marine cyanobacteria

(2013) Naama P. Dekel-Bird et al.   ENVIRONMENTAL MICROBIOLOGY

Structure and function of a cyanophage-encoded peptide deformylase

(2013) Jeremy A Frank et al.   ISME Journal

Genetic diversity in cultured and wild marine cyanomyoviruses reveals phosphorus stress as a strong selective agent

(2013) Libusha Kelly et al.   ISME Journal

Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone

(2013) Sangita Ganesh et al.   ISME Journal

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

Reconstruction of Novel Cyanobacterial Siphovirus Genomes from Mediterranean Metagenomic Fosmids

(2012) Carolina Megumi Mizuno et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Virus-driven nitrogen cycling enhances phytoplankton growth

(2012) EJ Shelford et al.   AQUATIC MICROBIAL ECOLOGY

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

(2012) Qinglu Zeng et al.   CURRENT BIOLOGY

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

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

Genomes of marine cyanopodoviruses reveal multiple origins of diversity

(2012) S. J. Labrie et al.   ENVIRONMENTAL MICROBIOLOGY

A novel lineage of myoviruses infecting cyanobacteria is widespread in the oceans

(2012) G. Sabehi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aligning short reads to reference alignments and trees

(2011) Simon A. Berger et al.   BIOINFORMATICS

Genome sequences of siphoviruses infecting marine Synechococcus unveil a diverse cyanophage group and extensive phage-host genetic exchanges

(2011) Sijun Huang et al.   ENVIRONMENTAL MICROBIOLOGY

Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea

(2011) Rachel J Parsons et al.   ISME Journal

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

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans

(2010) Rex R Malmstrom et al.   ISME Journal

Novel lineages of Prochlorococcus thrive within the oxygen minimum zone of the eastern tropical South Pacific

(2010) Paris Lavin et al.   Environmental Microbiology Reports

Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence ofSynechococcushost genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution

(2009) Andrew D. Millard et al.   ENVIRONMENTAL MICROBIOLOGY

Carrying photosynthesis genes increases ecological fitness of cyanophagein silico

(2009) Ferdi L. Hellweger   ENVIRONMENTAL MICROBIOLOGY

The genome and structural proteome of an ocean siphovirus: a new window into the cyanobacterial ‘mobilome’

(2009) Matthew B. Sullivan et al.   ENVIRONMENTAL MICROBIOLOGY

Photosystem I gene cassettes are present in marine virus genomes

(2009) Itai Sharon et al.   NATURE

Structural biology of the purine biosynthetic pathway

(2008) Y. Zhang et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Efficient Phage-Mediated Pigment Biosynthesis in Oceanic Cyanobacteria

(2008) Thorben Dammeyer et al.   CURRENT BIOLOGY

Portal protein diversity and phage ecology

(2008) Matthew B. Sullivan et al.   ENVIRONMENTAL MICROBIOLOGY

Phylogenetic and evolutionary relationships of RubisCO and the RubisCO-like proteins and the functional lessons provided by diverse molecular forms

(2008) F. R. Tabita et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Modeling the Fitness Consequences of a Cyanophage-Encoded Photosynthesis Gene

(2008) Jason G. Bragg et al.   PLoS One

Oxygen minimum zones (OMZs) in the modern ocean

(2008) A. Paulmier et al.   PROGRESS IN OCEANOGRAPHY