A virus or more in (nearly) every cell: ubiquitous networks of virus–host interactions in extreme environments

Viral ecology comes of age

(2017) Matthew B. Sullivan et al.   Environmental Microbiology Reports

Pseudomonas helleri sp. nov. and Pseudomonas weihenstephanensis sp. nov., isolated from raw cow's milk

(2016) M. von Neubeck et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences

(2016) Nathan A. Ahlgren et al.   NUCLEIC ACIDS RESEARCH

Healthy human gut phageome

(2016) Pilar Manrique et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs

(2015) Jacob H. Munson-McGee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysis

(2015) Benjamin Bolduc et al.   ISME Journal

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

(2015) Jessica M Labonté et al.   ISME Journal

Rising to the challenge: accelerated pace of discovery transforms marine virology

(2015) Jennifer R. Brum et al.   NATURE REVIEWS MICROBIOLOGY

Bacteriophages isolated from Lake Michigan demonstrate broad host-range across several bacterial phyla

(2015) Kema Malki et al.   Virology Journal

BiMat: aMATLABpackage to facilitate the analysis of bipartite networks

(2015) Cesar O. Flores et al.   Methods in Ecology and Evolution

Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population

(2015) Jessica M. Labonté et al.   Frontiers in Microbiology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

(2014) Li Deng et al.   NATURE

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

(2014) Simon Roux et al.   eLife

Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park

(2013) Mircea Podar et al.   Biology Direct

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

Short-term observations of marine bacterial and viral communities: patterns, connections and resilience

(2013) David M Needham et al.   ISME Journal

Single cell genomics: an individual look at microbes

(2012) Ramunas Stepanauskas   CURRENT OPINION IN MICROBIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Phage–bacteria infection networks

(2012) Joshua S. Weitz et al.   TRENDS IN MICROBIOLOGY

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

(2012) L. Deng et al.   mBio

Marine Viruses: Truth or Dare

(2011) Mya Breitbart   Annual Review of Marine Science

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

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

Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR

(2011) A. D. Tadmor et al.   SCIENCE

Use of Cellular CRISPR (Clusters of Regularly Interspaced Short Palindromic Repeats) Spacer-Based Microarrays for Detection of Viruses in Environmental Samples

(2010) J. C. Snyder et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Viruses manipulate the marine environment

(2009) Forest Rohwer et al.   NATURE

Biogeography of the Sulfolobus islandicus pan-genome

(2009) M. L. Reno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa

(2008) C. Winstanley et al.   GENOME RESEARCH