Phage puppet masters of the marine microbial realm

M Breitbart, C Bonnain, K Malki, NA Sawaya - Nature microbiology, 2018 - nature.com
Viruses numerically dominate our oceans; however, we have only just begun to document
the diversity, host range and infection dynamics of marine viruses, as well as the subsequent …

Computational approaches to predict bacteriophage–host relationships

RA Edwards, K McNair, K Faust, J Raes… - FEMS microbiology …, 2016 - academic.oup.com
Metagenomics has changed the face of virus discovery by enabling the accurate
identification of viral genome sequences without requiring isolation of the viruses. As a …

Next‐generation sequencing technologies for environmental DNA research

S Shokralla, JL Spall, JF Gibson… - Molecular …, 2012 - Wiley Online Library
Since 2005, advances in next‐generation sequencing technologies have revolutionized
biological science. The analysis of environmental DNA through the use of specific gene …

[PDF][PDF] Computational pan-genomics: status, promises and challenges

Briefings in bioinformatics, 2018 - academic.oup.com
Many disciplines, from human genetics and oncology to plant breeding, microbiology and
virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes …

Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes

K Moon, JH Jeon, I Kang, KS Park, K Lee, CJ Cha… - Microbiome, 2020 - Springer
Background Antibiotic resistance developed by bacteria is a significant threat to global
health. Antibiotic resistance genes (ARGs) spread across different bacterial populations …

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

FA Matsen, RB Kodner, EV Armbrust - BMC bioinformatics, 2010 - Springer
Background Likelihood-based phylogenetic inference is generally considered to be the most
reliable classification method for unknown sequences. However, traditional likelihood-based …

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

LF Jover, TC Effler, A Buchan, SW Wilhelm… - Nature Reviews …, 2014 - nature.com
In marine environments, virus-mediated lysis of host cells leads to the release of cellular
carbon and nutrients and is hypothesized to be a major driver of carbon recycling on a …

Marine viruses: truth or dare

M Breitbart - Annual review of marine science, 2012 - annualreviews.org
Over the past two decades, marine virology has progressed from a curiosity to an intensely
studied topic of critical importance to oceanography. At concentrations of approximately 10 …

The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology

BL Hurwitz, MB Sullivan - PloS one, 2013 - journals.plos.org
Bacteria and their viruses (phage) are fundamental drivers of many ecosystem processes
including global biogeochemistry and horizontal gene transfer. While databases and …

Viral metabolic reprogramming in marine ecosystems

BL Hurwitz, JM U'Ren - Current opinion in microbiology, 2016 - Elsevier
Highlights•Phages encode and express host-derived auxiliary metabolic genes
(AMGs).•AMGs encompass myriad metabolic (Class I) and peripheral (Class II) host …