Long-term stability and Red Queen-like strain dynamics in marine viruses

Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes

(2019) Ella T. Sieradzki et al.   Nature Communications

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Scaling read aligners to hundreds of threads on general-purpose processors

(2018) Ben Langmead et al.   BIOINFORMATICS

High parasite diversity accelerates host adaptation and diversification

(2018) A. Betts et al.   SCIENCE

FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data

(2018) Saima Sultana Tithi et al.   PeerJ

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Temporal dynamics of uncultured viruses: a new dimension in viral diversity

(2017) Ksenia Arkhipova et al.   ISME Journal

Diel cycling and long-term persistence of viruses in the ocean’s euphotic zone

(2017) Frank O. Aylward et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-virus genomics reveals hidden cosmopolitan and abundant viruses

(2017) Francisco Martinez-Hernandez et al.   Nature Communications

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

(2017) Jie Ren et al.   Microbiome

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

(2017) Yosuke Nishimura et al.   mSphere

Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer

(2016) Ann C. Gregory et al.   BMC GENOMICS

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

(2016) Matthew L Bendall et al.   ISME Journal

The diversity-generating benefits of a prokaryotic adaptive immune system

(2016) Stineke van Houte et al.   NATURE

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux 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

BFC: correcting Illumina sequencing errors

(2015) Heng Li   BIOINFORMATICS

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

What difference does it make if viruses are strain-, rather than species-specific?

(2015) T. Frede Thingstad et al.   Frontiers in Microbiology

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years

(2014) Jacob A Cram et al.   ISME Journal

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

(2014) Li Deng et al.   NATURE

MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data

(2014) Ikuo Uchiyama et al.   NUCLEIC ACIDS RESEARCH

Running with the Red Queen: the role of biotic conflicts in evolution

(2014) M. A. Brockhurst et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Antagonistic Coevolution of Marine Planktonic Viruses and Their Hosts

(2013) Jennifer B.H. Martiny et al.   Annual Review of Marine Science

Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight

(2013) Cheryl-Emiliane T Chow et al.   ISME Journal

Abundant SAR11 viruses in the ocean

(2013) Yanlin Zhao et al.   NATURE

Rapid evolution of the human gut virome

(2013) S. Minot 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

Seasonality and monthly dynamics of marine myovirus communities

(2012) Cheryl-Emiliane T. Chow et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Rapid diversification of coevolving marine Synechococcus and a virus

(2012) M. F. Marston et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Host-parasite coevolutionary arms races give way to fluctuating selection

(2011) Alex R. Hall et al.   ECOLOGY LETTERS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Viral and microbial community dynamics in four aquatic environments

(2010) Beltran Rodriguez-Brito et al.   ISME Journal

Antagonistic coevolution accelerates molecular evolution

(2010) Steve Paterson et al.   NATURE