Giant virus diversity and host interactions through global metagenomics

Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism

(2019) Disa Bäckström et al.   mBio

A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators

(2019) David M. Needham et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Taxon Richness of “Megaviridae” Exceeds those of Bacteria and Archaea in the Ocean

(2018) Tomoko Mihara et al.   MICROBES AND ENVIRONMENTS

A giant virus infecting green algae encodes key fermentation genes

(2018) Christopher R. Schvarcz et al.   VIROLOGY

Deciphering viral presences: two novel partial giant viruses detected in marine metagenome and in a mine drainage metagenome

(2018) Julien Andreani et al.   Virology Journal

Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere

(2018) Jônatas Abrahão et al.   Nature Communications

Molecular systematics of sturgeon nucleocytoplasmic large DNA viruses

(2018) Sharon Clouthier et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Ultrastructure of Meelsvirus: A nuclear virus of arrow worms (phylum Chaetognatha) producing giant “tailed” virions

(2018) George L. Shinn et al.   PLoS One

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes

(2018) David Paez-Espino et al.   NUCLEIC ACIDS RESEARCH

Genomic exploration of individual giant ocean viruses

(2017) William H Wilson et al.   ISME Journal

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton

(2017) Adam Monier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Giant viruses with an expanded complement of translation system components

(2017) Frederik Schulz et al.   SCIENCE

Variation in the Genetic Repertoire of Viruses Infecting Micromonas pusilla Reflects Horizontal Gene Transfer and Links to Their Environmental Distribution

(2017) Jan Finke et al.   Viruses-Basel

A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window

(2017) Lucie Gallot-Lavallée et al.   Viruses-Basel

290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology

(2017) Benjamin J. Tully et al.   PeerJ

A simple method to control over-alignment in the MAFFT multiple sequence alignment program

(2016) Kazutaka Katoh et al.   BIOINFORMATICS

Giant viruses come of age

(2016) Matthias G Fischer   CURRENT OPINION IN MICROBIOLOGY

Study of Gene Trafficking betweenAcanthamoebaand Giant Viruses Suggests an Undiscovered Family of Amoeba-Infecting Viruses

(2016) Florian Maumus et al.   Genome Biology and Evolution

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

IMG/M: integrated genome and metagenome comparative data analysis system

(2016) I-Min A. Chen et al.   NUCLEIC ACIDS RESEARCH

Giant Viruses of Amoebas: An Update

(2016) Sarah Aherfi et al.   Frontiers in Microbiology

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

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

Faustovirus, an Asfarvirus-Related New Lineage of Giant Viruses Infecting Amoebae

(2015) Dorine Gaëlle Reteno et al.   JOURNAL OF VIROLOGY

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Microbial and Animal Rhodopsins: Structures, Functions, and Molecular Mechanisms

(2013) Oliver P. Ernst et al.   CHEMICAL REVIEWS

Role of Ferric Reductases in Iron Acquisition and Virulence in the Fungal Pathogen Cryptococcus neoformans

(2013) Sanjay Saikia et al.   INFECTION AND IMMUNITY

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

(2013) Pascal Hingamp et al.   ISME Journal

Bacterial, archaeal and viral-like rhodopsins from the Red Sea

(2013) Alon Philosof et al.   Environmental Microbiology Reports

Route of NCLDV evolution: the genomic accordion

(2013) Jonathan Filée   Current Opinion in Virology

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

High-throughput isolation of giant viruses of theMimiviridaeandMarseilleviridaefamilies in the Tunisian environment

(2012) Mondher Boughalmi et al.   ENVIRONMENTAL MICROBIOLOGY

The Revised Classification of Eukaryotes

(2012) Sina M. Adl et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Iron Utilization in Marine Cyanobacteria and Eukaryotic Algae

(2012) Joe Morrissey et al.   Frontiers in Microbiology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Gene Exchange and the Origin of Giant Viruses

(2010) Jonathan Filée et al.   INTERVIROLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Mimivirus and Mimiviridae: Giant viruses with an increasing number of potential hosts, including corals and sponges

(2009) Jean-Michel Claverie et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution

(2009) Natalya Yutin et al.   Virology Journal

Giant viruses, giant chimeras: The multiple evolutionary histories of Mimivirus genes

(2008) David Moreira et al.   BMC EVOLUTIONARY BIOLOGY

Taxonomic distribution of large DNA viruses in the sea

(2008) Adam Monier et al.   GENOME BIOLOGY