Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses

Giant virus diversity and host interactions through global metagenomics

(2020) Frederik Schulz et al.   NATURE

Nitric oxide production and antioxidant function during viral infection of the coccolithophore Emiliania huxleyi

(2019) Brittany M. Schieler et al.   ISME Journal

Giant Viruses—Big Surprises

(2019) Nadav Brandes et al.   Viruses-Basel

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

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

Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes

(2019) Julien Guglielmini et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems

(2019) Amy E. Zimmerman et al.   NATURE REVIEWS MICROBIOLOGY

Unique structure and function of viral rhodopsins

(2019) Dmitry Bratanov et al.   Nature Communications

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

(2018) Tomoko Mihara et al.   MICROBES AND ENVIRONMENTS

Cryo-EM structure of a Marseilleviridae virus particle reveals a large internal microassembly

(2018) Kenta Okamoto et al.   VIROLOGY

A giant virus infecting green algae encodes key fermentation genes

(2018) Christopher R. Schvarcz et al.   VIROLOGY

Diversity and evolution of the emerging Pandoraviridae family

(2018) Matthieu Legendre et al.   Nature Communications

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

(2018) Jônatas Abrahão et al.   Nature Communications

Infection by a Giant Virus (AaV) Induces Widespread Physiological Reprogramming in Aureococcus anophagefferens CCMP1984 – A Harmful Bloom Algae

(2018) Mohammad Moniruzzaman et al.   Frontiers in Microbiology

GAPDH inhibits intracellular pathways during starvation for cellular energy homeostasis

(2018) Jia-Shu Yang et al.   NATURE

Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters

(2018) Yanze Li et al.   Viruses-Basel

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Pervasive iron limitation at subsurface chlorophyll maxima of the California Current

(2018) Shane L. Hogle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UFBoot2: Improving the Ultrafast Bootstrap Approximation

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

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

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

Marine Prasinoviruses and Their Tiny Plankton Hosts: A Review

(2017) Karen Weynberg et al.   Viruses-Basel

The analysis of translation-related gene set boosts debates around origin and evolution of mimiviruses

(2017) Jônatas Santos Abrahão et al.   PLoS Genetics

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Succinate, an intermediate in metabolism, signal transduction, ROS, hypoxia, and tumorigenesis

(2016) Laszlo Tretter et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Modulation of host ROS metabolism is essential for viral infection of a bloom-forming coccolithophore in the ocean

(2016) Uri Sheyn et al.   ISME Journal

Virocell Metabolism: Metabolic Innovations During Host–Virus Interactions in the Ocean

(2016) Shilo Rosenwasser et al.   TRENDS IN MICROBIOLOGY

The Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing

(2016) Jaime Iranzo et al.   mBio

Giant Viruses of Amoebas: An Update

(2016) Sarah Aherfi et al.   Frontiers in Microbiology

Recovering complete and draft population genomes from metagenome datasets

(2016) Naseer Sangwan et al.   Microbiome

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

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

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Central role for ferritin in the day/night regulation of iron homeostasis in marine phytoplankton

(2015) Hugo Botebol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution

(2015) Dominique Boeuf et al.   Database-The Journal of Biological Databases and Curation

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

The Megavirus Chilensis Cu,Zn-Superoxide Dismutase: the First Viral Structure of a Typical Cellular Copper Chaperone-Independent Hyperstable Dimeric Enzyme

(2014) Audrey Lartigue et al.   JOURNAL OF VIROLOGY

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

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

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

(2014) Luis F. Jover et al.   NATURE REVIEWS MICROBIOLOGY

Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology

(2014) M. Legendre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome of brown tide virus (AaV), the little giant of the Megaviridae, elucidates NCLDV genome expansion and host–virus coevolution

(2014) Mohammad Moniruzzaman et al.   VIROLOGY

Origin of giant viruses from smaller DNA viruses not from a fourth domain of cellular life

(2014) Natalya Yutin et al.   VIROLOGY

Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses

(2013) Adrien Jeanniard et al.   BMC GENOMICS

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

(2013) Pascal Hingamp et al.   ISME Journal

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

Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes

(2013) N. Philippe et al.   SCIENCE

“Marseilleviridae”, a new family of giant viruses infecting amoebae

(2012) Philippe Colson et al.   ARCHIVES OF VIROLOGY

Proteorhodopsin genes in giant viruses

(2012) Natalya Yutin et al.   Biology Direct

The virocell concept and environmental microbiology

(2012) Patrick Forterre   ISME Journal

Host-virus dynamics and subcellular controls of cell fate in a natural coccolithophore population

(2012) A. Vardi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Iron Utilization in Marine Cyanobacteria and Eukaryotic Algae

(2012) Joe Morrissey et al.   Frontiers in Microbiology

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Lausannevirus, a giant amoebal virus encoding histone doublets

(2011) Vincent Thomas et al.   ENVIRONMENTAL MICROBIOLOGY

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Bax Inhibitor 1 in apoptosis and disease

(2011) K S Robinson et al.   ONCOGENE

Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae

(2011) D. Arslan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Manipulation of cellular syntheses and the nature of viruses: The virocell concept

(2010) Patrick Forterre   COMPTES RENDUS CHIMIE

Classification and Determination of Possible Origins of ORFans through Analysis of Nucleocytoplasmic Large DNA Viruses

(2010) Mickaël Boyer et al.   INTERVIROLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Giant virus with a remarkable complement of genes infects marine zooplankton

(2010) M. G. Fischer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ten reasons to exclude viruses from the tree of life

(2009) David Moreira et al.   NATURE REVIEWS MICROBIOLOGY

Redefining viruses: lessons from Mimivirus

(2008) Didier Raoult et al.   NATURE REVIEWS MICROBIOLOGY

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE

Chlorella viruses evoke a rapid release of K+ from host cells during the early phase of infection

(2007) Monika Neupärtl et al.   VIROLOGY