Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics

Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer

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

Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China

(2016) Bin Ma et al.   ISME Journal

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

(2016) Matthew L Bendall et al.   ISME Journal

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

(2016) Sophie Weiss et al.   ISME Journal

Plankton networks driving carbon export in the oligotrophic ocean

(2016) Lionel Guidi et al.   NATURE

Host genome integration and giant virus-induced reactivation of the virophage mavirus

(2016) Matthias G. Fischer et al.   NATURE

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Invasive species triggers a massive loss of ecosystem services through a trophic cascade

(2016) Jake R. Walsh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A classification system for virophages and satellite viruses

(2015) Mart Krupovic et al.   ARCHIVES OF VIROLOGY

A new family of hybrid virophages from an animal gut metagenome

(2015) Natalya Yutin et al.   Biology Direct

A novel group of diverse Polinton-like viruses discovered by metagenome analysis

(2015) Natalya Yutin et al.   BMC BIOLOGY

Microcystin mcyA and mcyE Gene Abundances Are Not Appropriate Indicators of Microcystin Concentrations in Lakes

(2015) Lucas J. Beversdorf et al.   PLoS One

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses

(2014) Mart Krupovic et al.   Biology Direct

The virus of my virus is my friend: Ecological effects of virophage with alternative modes of coinfection

(2014) Bradford P. Taylor et al.   JOURNAL OF THEORETICAL BIOLOGY

Three Novel Virophage Genomes Discovered from Yellowstone Lake Metagenomes

(2014) Jinglie Zhou et al.   JOURNAL OF VIROLOGY

Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution

(2014) Mart Krupovic et al.   NATURE REVIEWS MICROBIOLOGY

Zamilon, a Novel Virophage with Mimiviridae Host Specificity

(2014) Morgan Gaia et al.   PLoS One

Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics

(2013) Alexander Eiler et al.   ENVIRONMENTAL MICROBIOLOGY

Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists

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

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

(2013) Pascal Hingamp et al.   ISME Journal

Diversity of Virophages in Metagenomic Data Sets

(2013) J. Zhou et al.   JOURNAL OF VIROLOGY

Broad Spectrum of Mimiviridae Virophage Allows Its Isolation Using a Mimivirus Reporter

(2013) Morgan Gaia et al.   PLoS One

Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes

(2013) S. Santini et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Temporal Dynamics and Decay of Putatively Allochthonous and Autochthonous Viral Genotypes in Contrasting Freshwater Lakes

(2012) Ian Hewson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Dynamic Viral Populations in Hypersaline Systems as Revealed by Metagenomic Assembly

(2012) Joanne B. Emerson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Efficient statistical significance approximation for local similarity analysis of high-throughput time series data

(2012) Li C. Xia et al.   BIOINFORMATICS

Molecular ecological network analyses

(2012) Ye Deng et al.   BMC BIOINFORMATICS

Related Giant Viruses in Distant Locations and Different Habitats: Acanthamoeba polyphaga moumouvirus Represents a Third Lineage of the Mimiviridae That Is Close to the Megavirus Lineage

(2012) Niyaz Yoosuf et al.   Genome Biology and Evolution

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Structure of Sputnik, a virophage, at 3.5-A resolution

(2012) X. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Easyfig: a genome comparison visualizer

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

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Viruses with More Than 1,000 Genes: Mamavirus, a New Acanthamoeba polyphagamimivirus Strain, and Reannotation of Mimivirus Genes

(2011) Philippe Colson et al.   Genome Biology and Evolution

A Guide to the Natural History of Freshwater Lake Bacteria

(2011) R. J. Newton et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Virophage control of antarctic algal host-virus dynamics

(2011) S. Yau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Virophage at the Origin of Large DNA Transposons

(2011) M. G. Fischer et al.   SCIENCE

The Neutral Theory of Molecular Evolution in the Genomic Era

(2010) Masatoshi Nei et al.   Annual Review of Genomics and Human Genetics

mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus

(2010) M. Legendre et al.   GENOME RESEARCH

Origin and Evolution of Eukaryotic Large Nucleo-Cytoplasmic DNA Viruses

(2010) Eugene V. Koonin et al.   INTERVIROLOGY

In This Issue

(2010)   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mimivirus and its Virophage

(2009) Jean-Michel Claverie et al.   Annual Review of Genetics

Identification of ribosomal RNA genes in metagenomic fragments

(2009) Ying Huang et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Recombination and microdiversity in coastal marine cyanophages

(2009) Marcia F. Marston et al.   ENVIRONMENTAL MICROBIOLOGY

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

(2008) G. Lima-Mendez et al.   MOLECULAR BIOLOGY AND EVOLUTION

The virophage as a unique parasite of the giant mimivirus

(2008) Bernard La Scola et al.   NATURE

Temporal variation in freshwater viral and bacterial community composition

(2007) DAVID LYMER et al.   FRESHWATER BIOLOGY