A planarian nidovirus expands the limits of RNA genome size

Using Metagenomics to Characterize an Expanding Virosphere

(2018) Yong-Zhen Zhang et al.   CELL

The evolutionary history of vertebrate RNA viruses

(2018) Mang Shi et al.   NATURE

An “Old” protein with a new story: Coronavirus endoribonuclease is important for evading host antiviral defenses

(2018) Xufang Deng et al.   VIROLOGY

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

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

MERS-CoV 4b protein interferes with the NF-κB-dependent innate immune response during infection

(2018) Javier Canton et al.   PLoS Pathogens

The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms

(2018) Markus Alexander Grohme et al.   NATURE

Fatal swine acute diarrhoea syndrome caused by an HKU2-related coronavirus of bat origin

(2018) Peng Zhou et al.   NATURE

Polycipiviridae: a proposed new family of polycistronic picorna-like RNA viruses

(2017) Ingrida Olendraite et al.   JOURNAL OF GENERAL VIROLOGY

A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations

(2017) Emily J. Remnant et al.   JOURNAL OF VIROLOGY

Structural and molecular basis of mismatch correction and ribavirin excision from coronavirus RNA

(2017) François Ferron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple origins of viral capsid proteins from cellular ancestors

(2017) Mart Krupovic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expanded subgenomic mRNA transcriptome and coding capacity of a nidovirus

(2017) Han Di 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

MERS-CoV Accessory ORFs Play Key Role for Infection and Pathogenesis

(2017) Vineet D. Menachery et al.   mBio

Protein-directed ribosomal frameshifting temporally regulates gene expression

(2017) Sawsan Napthine et al.   Nature Communications

Crystal structure of Middle East respiratory syndrome coronavirus helicase

(2017) Wei Hao et al.   PLoS Pathogens

Bioinformatics and functional analyses of coronavirus nonstructural proteins involved in the formation of replicative organelles

(2016) Benjamin W. Neuman   ANTIVIRAL RESEARCH

Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2016)

(2016) Michael J. Adams et al.   ARCHIVES OF VIROLOGY

Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses

(2016) Jordon Rahaman et al.   Genome Biology and Evolution

Identification and Characterization of a Ribose 2′-O-Methyltransferase Encoded by the Ronivirus Branch of Nidovirales

(2016) Cong Zeng et al.   JOURNAL OF VIROLOGY

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

GenBank

(2016) Dennis A. Benson 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

GPCRs Direct Germline Development and Somatic Gonad Function in Planarians

(2016) Amir Saberi et al.   PLOS BIOLOGY

A Transcriptomic-Phylogenomic Analysis of the Evolutionary Relationships of Flatworms

(2015) Bernhard Egger et al.   CURRENT BIOLOGY

SmedGD 2.0: TheSchmidtea mediterraneagenome database

(2015) Sofia M.C. Robb et al.   GENESIS

Discovery of a novel nidovirus in cattle with respiratory disease

(2015) Rafal Tokarz et al.   JOURNAL OF GENERAL VIROLOGY

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

Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerase-containing protein of all nidoviruses

(2015) Kathleen C. Lehmann et al.   NUCLEIC ACIDS RESEARCH

PlanMine – a mineable resource of planarian biology and biodiversity

(2015) Holger Brandl 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

JPred4: a protein secondary structure prediction server

(2015) Alexey Drozdetskiy et al.   NUCLEIC ACIDS RESEARCH

Structural basis and functional analysis of the SARS coronavirus nsp14–nsp10 complex

(2015) Yuanyuan Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

What we know but do not understand about nidovirus helicases

(2015) Kathleen C. Lehmann et al.   VIRUS RESEARCH

Incorporation of Spike and Membrane Glycoproteins into Coronavirus Virions

(2015) Makoto Ujike et al.   Viruses-Basel

Continuous and Discontinuous RNA Synthesis in Coronaviruses

(2015) Isabel Sola et al.   Annual Review of Virology

The RNA shapes studio

(2014) S. Janssen et al.   BIOINFORMATICS

Novel divergent nidovirus in a python with pneumonia

(2014) R. Bodewes et al.   JOURNAL OF GENERAL VIROLOGY

Viral Phosphodiesterases That Antagonize Double-Stranded RNA Signaling to RNase L by Degrading 2-5A

(2014) Robert H. Silverman et al.   JOURNAL OF INTERFERON AND CYTOKINE RESEARCH

Characterization of an Alphamesonivirus 3C-Like Protease Defines a Special Group of Nidovirus Main Proteases

(2014) S. Blanck et al.   JOURNAL OF VIROLOGY

Receptor Recognition Mechanisms of Coronaviruses: a Decade of Structural Studies

(2014) Fang Li   JOURNAL OF VIROLOGY

Systems Biology Perspectives on Minimal and Simpler Cells

(2014) J. C. Xavier et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Preparation of the planarian Schmidtea mediterranea for high-resolution histology and transmission electron microscopy

(2014) John L Brubacher et al.   Nature Protocols

NCBI Viral Genomes Resource

(2014) J. Rodney Brister et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities

(2014) Lorenzo Subissi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Middle East respiratory syndrome coronavirus: transmission and phylogenetic evolution

(2014) Jaffar A. Al-Tawfiq et al.   TRENDS IN MICROBIOLOGY

Does form meet function in the coronavirus replicative organelle?

(2014) Benjamin W. Neuman et al.   TRENDS IN MICROBIOLOGY

Membrane proteins of arterivirus particles: Structure, topology, processing and function

(2014) Michael Veit et al.   VIRUS RESEARCH

Ball Python Nidovirus: a Candidate Etiologic Agent for Severe Respiratory Disease in Python regius

(2014) M. D. Stenglein et al.   mBio

Thinking Outside the Triangle: Replication Fidelity of the Largest RNA Viruses

(2014) Everett Clinton Smith et al.   Annual Review of Virology

An Extracellular Serine/Threonine-Rich Protein from Lactobacillus plantarum NCIMB 8826 Is a Novel Aggregation-Promoting Factor with Affinity to Mucin

(2013) Arancha Hevia et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

In situ hybridization protocol for enhanced detection of gene expression in the planarian Schmidtea mediterranea

(2013) Ryan S King et al.   BMC DEVELOPMENTAL BIOLOGY

Looking for trees in the forest: summary tree from posterior samples

(2013) Joseph Heled et al.   BMC EVOLUTIONARY BIOLOGY

Arterivirus molecular biology and pathogenesis

(2013) E. J. Snijder et al.   JOURNAL OF GENERAL VIROLOGY

Identification and Characterization of Genetically Divergent Members of the Newly Established Family Mesoniviridae

(2013) F. Zirkel et al.   JOURNAL OF VIROLOGY

Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase

(2013) Z. Deng et al.   NUCLEIC ACIDS RESEARCH

Rbm20 regulates titin alternative splicing as a splicing repressor

(2013) Shijun Li et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

(2013) N. Philippe et al.   SCIENCE

A new nidovirus (NamDinh virus NDiV): Its ultrastructural characterization in the C6/36 mosquito cell line

(2013) Nguyen Thanh Thuy et al.   VIROLOGY

Infectious Bronchitis Virus Generates Spherules from Zippered Endoplasmic Reticulum Membranes

(2013) H. J. Maier et al.   mBio

A virocentric perspective on the evolution of life

(2013) Eugene V Koonin et al.   Current Opinion in Virology

The Footprint of Genome Architecture in the Largest Genome Expansion in RNA Viruses

(2013) Chris Lauber et al.   PLoS Pathogens

Coronaviruses Lacking Exoribonuclease Activity Are Susceptible to Lethal Mutagenesis: Evidence for Proofreading and Potential Therapeutics

(2013) Everett Clinton Smith et al.   PLoS Pathogens

Mesoniviridae: a proposed new family in the order Nidovirales formed by a single species of mosquito-borne viruses

(2012) Chris Lauber et al.   ARCHIVES OF VIROLOGY

NF-κB: where did it come from and why?

(2012) Thomas D. Gilmore et al.   IMMUNOLOGICAL REVIEWS

Non-canonical translation in RNA viruses

(2012) A. E. Firth et al.   JOURNAL OF GENERAL VIROLOGY

Arterivirus Minor Envelope Proteins Are a Major Determinant of Viral Tropism in Cell Culture

(2012) D. Tian et al.   JOURNAL OF VIROLOGY

Partitioning the Genetic Diversity of a Virus Family: Approach and Evaluation through a Case Study of Picornaviruses

(2012) C. Lauber et al.   JOURNAL OF VIROLOGY

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Platyhelminth Venom Allergen-Like (VAL) proteins: revealing structural diversity, class-specific features and biological associations across the phylum

(2012) IAIN W. CHALMERS et al.   PARASITOLOGY

RNA 3'-end mismatch excision by the severe acute respiratory syndrome coronavirus nonstructural protein nsp10/nsp14 exoribonuclease complex

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

Crystal Structure of the Pestivirus Envelope Glycoprotein Erns and Mechanistic Analysis of Its Ribonuclease Activity

(2012) Thomas Krey et al.   STRUCTURE

SARS coronavirus pathogenesis: host innate immune responses and viral antagonism of interferon

(2012) Allison L Totura et al.   Current Opinion in Virology

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba 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

Schmidtea mediterraneaphylogeography: an old species surviving on a few Mediterranean islands?

(2011) Eva M Lázaro et al.   BMC EVOLUTIONARY BIOLOGY

Immunosuppression induced by expression of a viral RNase enhances susceptibility of Plutella xylostella to microbial pesticides

(2011) Bokri Park et al.   Insect Science

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Modulation of NF-κB signalling by microbial pathogens

(2011) Masmudur M. Rahman et al.   NATURE REVIEWS MICROBIOLOGY

Which came first, the virus or the cell?

(2011) V. I. Agol   PALEONTOLOGICAL JOURNAL

RNA-Binding Domain in the Nucleocapsid Protein of Gill-Associated Nidovirus of Penaeid Shrimp

(2011) Chumporn Soowannayan et al.   PLoS One

An Insect Nidovirus Emerging from a Primary Tropical Rainforest

(2011) F. Zirkel et al.   mBio

Discovery of the First Insect Nidovirus, a Missing Evolutionary Link in the Emergence of the Largest RNA Virus Genomes

(2011) Phan Thi Nga et al.   PLoS Pathogens

Biochemical and Structural Insights into the Mechanisms of SARS Coronavirus RNA Ribose 2′-O-Methylation by nsp16/nsp10 Protein Complex

(2011) Yu Chen et al.   PLoS Pathogens

SLIIME-SECRETING CELLS OF PLANARIANS

(2010) Knud Jørgen Pedersen   Annals of the New York Academy of Sciences

Practical application of bioinformatics by the multidisciplinary VIZIER consortium

(2010) Alexander E. Gorbalenya et al.   ANTIVIRAL RESEARCH

The use of lectins as markers for differentiated secretory cells in planarians

(2010) Ricardo M. Zayas et al.   DEVELOPMENTAL DYNAMICS

A functional genomic screen in planarians identifies novel regulators of germ cell development

(2010) Y. Wang et al.   GENES & DEVELOPMENT

Characterization of Bafinivirus Main Protease Autoprocessing Activities

(2010) R. Ulferts et al.   JOURNAL OF VIROLOGY

Viral Mutation Rates

(2010) R. Sanjuan et al.   JOURNAL OF VIROLOGY

Why genes overlap in viruses

(2010) N. Chirico et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

T2 Family ribonucleases: ancient enzymes with diverse roles

(2010) Natalie Luhtala et al.   TRENDS IN BIOCHEMICAL SCIENCES

Evolution of the mutation rate

(2010) Michael Lynch   TRENDS IN GENETICS

In Vitro Reconstitution of SARS-Coronavirus mRNA Cap Methylation

(2010) Mickaël Bouvet et al.   PLoS Pathogens

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Coronaviruses post-SARS: update on replication and pathogenesis

(2009) Stanley Perlman et al.   NATURE REVIEWS MICROBIOLOGY

Functional screen reveals SARS coronavirus nonstructural protein nsp14 as a novel cap N7 methyltransferase

(2009) Y. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional diversity of ankyrin repeats in microbial proteins

(2009) Souhaila Al-Khodor et al.   TRENDS IN MICROBIOLOGY

Picornavirales, a proposed order of positive-sense single-stranded RNA viruses with a pseudo-T = 3 virion architecture

(2008) Olivier Le Gall et al.   ARCHIVES OF VIROLOGY

The role of programmed-1 ribosomal frameshifting in coronavirus propagation

(2008) Ewan et al.   Frontiers in Bioscience-Landmark

Coronavirus Nonstructural Protein 16 Is a Cap-0 Binding Enzyme Possessing (Nucleoside-2'O)-Methyltransferase Activity

(2008) E. Decroly et al.   JOURNAL OF VIROLOGY

Pacing a small cage: mutation and RNA viruses

(2008) Robert Belshaw et al.   TRENDS IN ECOLOGY & EVOLUTION

SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum

(2008) Kèvin Knoops et al.   PLOS BIOLOGY