Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome

The Potyviruses: An Evolutionary Synthesis Is Emerging

(2020) Adrian J. Gibbs et al.   Viruses-Basel

Expansion of known ssRNA phage genomes: From tens to over a thousand

(2020) J. Callanan et al.   Science Advances

Deep Roots and Splendid Boughs of the Global Plant Virome

(2020) Valerian V. Dolja et al.   Annual Review of Phytopathology

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

(2019) Disa Bäckström et al.   mBio

Classify viruses — the gain is worth the pain

(2019) Jens H. Kuhn et al.   NATURE

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Expanding the RNA Virosphere by Unbiased Metagenomics

(2019) Yong-Zhen Zhang et al.   Annual Review of Virology

Marine RNA Virus Quasispecies Are Distributed throughout the Oceans

(2019) Marli Vlok et al.   mSphere

Evolution and ecology of plant viruses

(2019) Pierre Lefeuvre et al.   NATURE REVIEWS MICROBIOLOGY

Silicon limitation facilitates virus infection and mortality of marine diatoms

(2019) Chana F. Kranzler et al.   Nature Microbiology

The evolutionary history of vertebrate RNA viruses

(2018) Mang Shi et al.   NATURE

A decade of RNA virus metagenomics is (not) enough

(2018) Alexander L. Greninger   VIRUS RESEARCH

Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer

(2018) Valerian V. Dolja et al.   VIRUS RESEARCH

New insight into the RNA aquatic virosphere via viromics

(2018) Alexander Culley   VIRUS RESEARCH

Evolutionary and ecological links between plant and fungal viruses

(2018) Marilyn J. Roossinck   NEW PHYTOLOGIST

Viruses of Eukaryotic Algae: Diversity, Methods for Detection, and Future Directions

(2018) Samantha Coy et al.   Viruses-Basel

Expansion of the metazoan virosphere: progress, pitfalls, and prospects

(2018) Darren J Obbard   Current Opinion in Virology

Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes

(2018) Fergal M. Waldron et al.   PLoS Genetics

Transcriptional recording by CRISPR spacer acquisition from RNA

(2018) Florian Schmidt et al.   NATURE

Discovery of highly divergent lineages of plant-associated astro-like viruses sheds light on the emergence of potyviruses

(2018) Chris Lauber et al.   VIRUS RESEARCH

Origins and Evolution of the Global RNA Virome

(2018) Yuri I. Wolf et al.   mBio

ICTV Virus Taxonomy Profile: Dicistroviridae

(2017) S. M Valles et al.   JOURNAL OF GENERAL VIROLOGY

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Virus taxonomy in the age of metagenomics

(2017) Peter Simmonds et al.   NATURE REVIEWS MICROBIOLOGY

EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies

(2017) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

Viral discovery and diversity in trypanosomatid protozoa with a focus on relatives of the human parasiteLeishmania

(2017) Danyil Grybchuk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Statoviruses, A novel taxon of RNA viruses present in the gastrointestinal tracts of diverse mammals

(2017) Andrew B. Janowski et al.   VIROLOGY

The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes

(2017) Sergey A. Shmakov et al.   mBio

Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics

(2017) Mohammad Moniruzzaman et al.   Nature Communications

Studies on the Virome of the Entomopathogenic Fungus Beauveria bassiana Reveal Novel dsRNA Elements and Mild Hypervirulence

(2017) Ioly Kotta-Loizou et al.   PLoS Pathogens

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut

(2017) Natalya Yutin et al.   Nature Microbiology

Potyvirus virion structure shows conserved protein fold and RNA binding site in ssRNA viruses

(2017) Miguel Zamora et al.   Science Advances

RNA viruses as major contributors to Antarctic virioplankton

(2016) Jaclyn A. Miranda et al.   ENVIRONMENTAL MICROBIOLOGY

Zoosporic parasites infecting marine diatoms – A black box that needs to be opened

(2016) Bettina Scholz et al.   Fungal Ecology

Identification of Diverse Mycoviruses through Metatranscriptomics Characterization of the Viromes of Five Major Fungal Plant Pathogens

(2016) Shin-Yi Lee Marzano et al.   JOURNAL OF VIROLOGY

Redefining the invertebrate RNA virosphere

(2016) Mang Shi et al.   NATURE

Uniclust databases of clustered and deeply annotated protein sequences and alignments

(2016) Milot Mirdita et al.   NUCLEIC ACIDS RESEARCH

West African Anopheles gambiae mosquitoes harbor a taxonomically diverse virome including new insect-specific flaviviruses, mononegaviruses, and totiviruses

(2016) Joseph R. Fauver et al.   VIROLOGY

Hyperexpansion of RNA Bacteriophage Diversity

(2016) Siddharth R. Krishnamurthy et al.   PLOS BIOLOGY

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

(2015) Natalya Yutin et al.   BMC BIOLOGY

Divergent Viruses Discovered in Arthropods and Vertebrates Revise the Evolutionary History of the Flaviviridae and Related Viruses

(2015) Mang Shi et al.   JOURNAL OF VIROLOGY

Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake

(2015) A. López-Bueno et al.   MOLECULAR ECOLOGY

Rising to the challenge: accelerated pace of discovery transforms marine virology

(2015) Jennifer R. Brum et al.   NATURE REVIEWS MICROBIOLOGY

Origins and evolution of viruses of eukaryotes: The ultimate modularity

(2015) Eugene V. Koonin et al.   VIROLOGY

The Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster

(2015) Claire L. Webster et al.   PLOS BIOLOGY

The Structure of the RNA-Dependent RNA Polymerase of a Permutotetravirus Suggests a Link between Primer-Dependent and Primer-Independent Polymerases

(2015) Diego S. Ferrero et al.   PLoS Pathogens

The near-atomic cryoEM structure of a flexible filamentous plant virus shows homology of its coat protein with nucleoproteins of animal viruses

(2015) Xabier Agirrezabala et al.   eLife

Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses

(2015) Ci-Xiu Li et al.   eLife

Biogeography of Viruses in the Sea

(2015) Cheryl-Emiliane T. Chow et al.   Annual Review of Virology

Discovery of Two Novel Viruses Expands the Diversity of Single-Stranded DNA and Single-Stranded RNA Viruses Infecting a Cosmopolitan Marine Diatom

(2014) Kei Kimura et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

High temporal and spatial diversity in marine RNA viruses implies that they have an important role in mortality and structuring plankton communities

(2014) Julia A. Gustavsen et al.   Frontiers in Microbiology

Identification of Novel Positive-Strand RNA Viruses by Metagenomic Analysis of Archaea-Dominated Yellowstone Hot Springs

(2012) B. Bolduc et al.   JOURNAL OF VIROLOGY

High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage

(2012) T. F. F. Ng et al.   JOURNAL OF VIROLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

The nucleotide sequence and genome organization of Plasmopara halstedii virus

(2011) Marion Heller-Dohmen et al.   Virology Journal

Common origins and host-dependent diversity of plant and animal viromes

(2011) Valerian V Dolja et al.   Current Opinion in Virology

Natural and Experimental Infection of Caenorhabditis Nematodes by Novel Viruses Related to Nodaviruses

(2011) Marie-Anne Félix et al.   PLOS BIOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Analysis of High-Throughput Sequencing and Annotation Strategies for Phage Genomes

(2010) Matthew R. Henn et al.   PLoS One

Isolation and Characterization of a Single-Stranded RNA Virus Infecting the Bloom-Forming Diatom Chaetoceros socialis

(2009) Y. Tomaru et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomic analysis of viruses in reclaimed water

(2009) Karyna Rosario et al.   ENVIRONMENTAL MICROBIOLOGY

Permutation of the active site of putative RNA-dependent RNA polymerase in a newly identified species of plant alpha-like virus

(2009) Sead Sabanadzovic et al.   VIROLOGY

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

(2009) Natalya Yutin et al.   Virology Journal

Isolation and Characterization of a Single-Stranded RNA Virus Infecting the Marine Planktonic Diatom Chaetoceros tenuissimus Meunier

(2008) Y. Shirai et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Dinoflagellates, diatoms, and their viruses

(2008) Keizo Nagasaki   JOURNAL OF MICROBIOLOGY