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

Contrasting genomic patterns and infection strategies of two co-existingBacteroidetespodovirus genera

(2014) Karin Holmfeldt et al.   ENVIRONMENTAL MICROBIOLOGY

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

(2014) Li Deng et al.   NATURE

The elemental composition of virus particles: implications for marine biogeochemical cycles

(2014) Luis F. Jover et al.   NATURE REVIEWS MICROBIOLOGY

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

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

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

(2014) Simon Roux et al.   eLife

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

Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton

(2013) Helen F Schmidt et al.   ISME Journal

Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle

(2013) Jody J Wright et al.   ISME Journal

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

(2013) Sergey Nurk et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Abundant SAR11 viruses in the ocean

(2013) Yanlin Zhao et al.   NATURE

The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology

(2013) Bonnie L. Hurwitz et al.   PLoS One

Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans

(2013) I. Kang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

(2013) B. K. Swan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Twelve previously unknown phage genera are ubiquitous in global oceans

(2013) K. Holmfeldt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expanding the Marine Virosphere Using Metagenomics

(2013) Carolina Megumi Mizuno et al.   PLoS Genetics

Regional Variation in Lytic and Lysogenic Viral Infection in the Southern Ocean and Its Contribution to Biogeochemical Cycling

(2012) Claire Evans et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Single cell genomics: an individual look at microbes

(2012) Ramunas Stepanauskas   CURRENT OPINION IN MICROBIOLOGY

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

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

Genomic sequencing of uncultured microorganisms from single cells

(2012) Roger S. Lasken   NATURE REVIEWS MICROBIOLOGY

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

(2012) Sajia Akhter et al.   NUCLEIC ACIDS RESEARCH

PIPS: Pathogenicity Island Prediction Software

(2012) Siomar C. Soares et al.   PLoS One

Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia

(2012) Manuel Martinez-Garcia et al.   PLoS One

Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging

(2012) L. Deng et al.   mBio

Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria

(2012) Jana Grote et al.   Standards in Genomic Sciences

Marine Viruses: Truth or Dare

(2011) Mya Breitbart   Annual Review of Marine Science

Cultivated Single-Stranded DNA Phages That Infect Marine Bacteroidetes Prove Difficult To Detect with DNA-Binding Stains

(2011) Karin Holmfeldt et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba 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

Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome

(2011) Margret E. Berg Miller et al.   ENVIRONMENTAL MICROBIOLOGY

Using CRISPRs as a metagenomic tool to identify microbial hosts of a diffuse flow hydrothermal vent viral assemblage

(2011) Rika E. Anderson et al.   FEMS MICROBIOLOGY ECOLOGY

Phylogenomic Evidence for the Presence of a Flagellum and cbb3 Oxidase in the Free-Living Mitochondrial Ancestor

(2011) D. Sassera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Statistical structure of host-phage interactions

(2011) C. O. Flores et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists

(2011) H. S. Yoon et al.   SCIENCE

Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR

(2011) A. D. Tadmor et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Complete Genome Sequence of "Candidatus Puniceispirillum marinum" IMCC1322, a Representative of the SAR116 Clade in the Alphaproteobacteria

(2010) H.-M. Oh et al.   JOURNAL OF BACTERIOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Phylogenetic Analysis Indicates Evolutionary Diversity and Environmental Segregation of Marine Podovirus DNA Polymerase Gene Sequences

(2009) J. M. Labonte et al.   APPLIED AND 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

Assembling the Marine Metagenome, One Cell at a Time

(2009) Tanja Woyke et al.   PLoS One

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Prophinder: a computational tool for prophage prediction in prokaryotic genomes

(2008) Gipsi Lima-Mendez et al.   BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas?

(2008) John H Paul   ISME Journal

Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression

(2008) Lauren McDaniel et al.   PLoS One

Comparative genomics of the mycobacteriophages: insights into bacteriophage evolution

(2008) Graham F. Hatfull et al.   RESEARCH IN MICROBIOLOGY

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY