Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes

PHANOTATE: a novel approach to gene identification in phage genomes

(2019) Katelyn McNair et al.   BIOINFORMATICS

Cholera toxin promotes pathogen acquisition of host-derived nutrients

(2019) Fabian Rivera-Chávez et al.   NATURE

Biophysical and physiological processes causing oxygen loss from coral reefs

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Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts

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Phage–host population dynamics promotes prophage acquisition in bacteria with innate immunity

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Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton

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Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans

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Bordetella bronchiseptica exploits the complex life cycle of Dictyostelium discoideum as an amplifying transmission vector

(2017) Dawn L. Taylor-Mulneix et al.   PLOS BIOLOGY

Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters

(2017) Mario López-Pérez et al.   PLoS Genetics

Bacterial Community Associated with the Reef Coral Mussismilia braziliensis's Momentum Boundary Layer over a Diel Cycle

(2017) Cynthia B. Silveira et al.   Frontiers in Microbiology

Bacteriophage evolution differs by host, lifestyle and genome

(2017) Travis N. Mavrich et al.   Nature Microbiology

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

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Lytic to temperate switching of viral communities

(2016) B. Knowles et al.   NATURE

Uncovering Earth’s virome

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Shifting white pox aetiologies affectingAcropora palmatain the Florida Keys, 1994–2014

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Viruses as Winners in the Game of Life

(2016) Ana Georgina Cobián Güemes et al.   Annual Review of Virology

Global microbialization of coral reefs

(2016) Andreas F. Haas et al.   Nature Microbiology

Piggyback-the-Winner in host-associated microbial communities

(2016) Cynthia B Silveira et al.   npj Biofilms and Microbiomes

Microbial and sponge loops modify fish production in phase-shifting coral reefs

(2015) Cynthia B. Silveira et al.   ENVIRONMENTAL MICROBIOLOGY

A new perspective on lysogeny: prophages as active regulatory switches of bacteria

(2015) Ron Feiner et al.   NATURE REVIEWS MICROBIOLOGY

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

From cholera to corals: Viruses as drivers of virulence in a major coral bacterial pathogen

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

(2015) William Cenens et al.   PLoS Genetics

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

(2015) Simon Roux et al.   eLife

Anvi’o: an advanced analysis and visualization platform for ‘omics data

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Diversity and ecological structure of vibrios in benthic and pelagic habitats along a latitudinal gradient in the Southwest Atlantic Ocean

(2015) Luciane A. Chimetto Tonon et al.   PeerJ

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses

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Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors

(2014) L. W. Kelly et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pervasive domestication of defective prophages by bacteria

(2014) L.-M. Bobay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Revisiting the genome packaging in viruses with lessons from the “Giants”

(2014) Venkata Chelikani et al.   VIROLOGY

GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

(2013) Bruno Contreras-Moreira et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomic Analysis of Healthy and White Plague-Affected Mussismilia braziliensis Corals

(2013) Gizele D. Garcia et al.   MICROBIAL ECOLOGY

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

CRISPRTarget

(2013) Ambarish Biswas et al.   RNA Biology

Expanding the Marine Virosphere Using Metagenomics

(2013) Carolina Megumi Mizuno et al.   PLoS Genetics

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Abrolhos Bank Reef Health Evaluated by Means of Water Quality, Microbial Diversity, Benthic Cover, and Fish Biomass Data

(2012) Thiago Bruce et al.   PLoS One

Assessing Coral Reefs on a Pacific-Wide Scale Using the Microbialization Score

(2012) Tracey McDole et al.   PLoS One

Unseen players shape benthic competition on coral reefs

(2012) Katie L. Barott et al.   TRENDS IN MICROBIOLOGY

Genomic and proteomic analyses of the coral pathogen Vibrio coralliilyticus reveal a diverse virulence repertoire

(2011) Eidy de O Santos et al.   ISME Journal

Identification of Genes and Genomic Islands Correlated with High Pathogenicity in Streptococcus suis Using Whole Genome Tilling Microarrays

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Evolutionary microbial genomics: insights into bacterial host adaptation

(2010) Christina Toft et al.   NATURE REVIEWS GENETICS

Horizontal Gene Transfer of the Secretome Drives the Evolution of Bacterial Cooperation and Virulence

(2009) Teresa Nogueira et al.   CURRENT BIOLOGY

Microbial disease and the coral holobiont

(2009) David G. Bourne et al.   TRENDS IN MICROBIOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

CHANGES IN THE MORPHOLOGY AND POLYSACCHARIDE CONTENT OFMICROCYSTIS AERUGINOSA(CYANOBACTERIA) DURING FLAGELLATE GRAZING

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Rates of evolutionary change in viruses: patterns and determinants

(2008) Siobain Duffy et al.   NATURE REVIEWS GENETICS

Microbial Ecology of Four Coral Atolls in the Northern Line Islands

(2008) Elizabeth A. Dinsdale et al.   PLoS One