Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes

The Novel Halovirus Hardycor1, and the Presence of Active (Induced) Proviruses in Four Haloarchaea

(2021) Mike Dyall-Smith et al.   Genes

Massive expansion of human gut bacteriophage diversity

(2021) Luis F. Camarillo-Guerrero et al.   CELL

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Accurate prediction of protein structures and interactions using a three-track neural network

(2021) Minkyung Baek et al.   SCIENCE

Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea

(2021) Friedhelm Pfeiffer et al.   Genes

Global Organization and Proposed Megataxonomy of the Virus World

(2020) Eugene V. Koonin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Phage diversity, genomics and phylogeny

(2020) Moïra B. Dion et al.   NATURE REVIEWS MICROBIOLOGY

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

(2020) J. Callanan et al.   Science Advances

New virus isolates from Italian hydrothermal environments underscore the biogeographic pattern in archaeal virus communities

(2020) Diana P. Baquero et al.   ISME Journal

Two Cobalt Chelatase Subunits Can Be Generated from a Single chlD Gene via Programed Frameshifting

(2020) Ivan V Antonov   MOLECULAR BIOLOGY AND EVOLUTION

Comparative Genomics of Two New HF1-like Haloviruses

(2020) Mike Dyall-Smith et al.   Genes

The LUCA and its complex virome

(2020) Mart Krupovic et al.   NATURE REVIEWS MICROBIOLOGY

Abortive Infection: Bacterial Suicide as an Antiviral Immune Strategy

(2020) Anna Lopatina et al.   Annual Review of Virology

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

(2020) Yuri I. Wolf et al.   Nature Microbiology

The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut

(2020) Ann C. Gregory et al.   Cell Host & Microbe

The first head‐tailed virus, MFTV1 , infecting hyperthermophilic methanogenic deep‐sea archaea

(2020) Sarah Thiroux et al.   ENVIRONMENTAL MICROBIOLOGY

Halobacterium salinarum virus ChaoS9, a Novel Halovirus Related to PhiH1 and PhiCh1

(2019) Mike Dyall-Smith et al.   Genes

Numerous cultivated and uncultivated viruses encode ribosomal proteins

(2019) Carolina M. Mizuno et al.   Nature Communications

Host-hijacking and planktonic piracy: how phages command the microbial high seas

(2019) Joanna Warwick-Dugdale et al.   Virology Journal

Novel haloarchaeal viruses from Lake Retba infecting Haloferax and Halorubrum species

(2019) Carolina M. Mizuno et al.   ENVIRONMENTAL MICROBIOLOGY

Integrated mobile genetic elements in Thaumarchaeota

(2019) Mart Krupovic et al.   ENVIRONMENTAL MICROBIOLOGY

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages

(2019) Jakub Barylski et al.   SYSTEMATIC BIOLOGY

The amazing HK97 fold: versatile results of modest differences

(2019) Robert L Duda et al.   Current Opinion in Virology

Portal Protein: The Orchestrator of Capsid Assembly for the dsDNA Tailed Bacteriophages and Herpesviruses

(2019) Corynne L. Dedeo et al.   Annual Review of Virology

The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific

(2019) Andrey N. Shkoporov et al.   Cell Host & Microbe

7-Deazaguanine modifications protect phage DNA from host restriction systems

(2019) Geoffrey Hutinet et al.   Nature Communications

Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy

(2018) Pakorn Aiewsakun et al.   JOURNAL OF GENERAL VIROLOGY

Evolutionary insights into Trm112-methyltransferase holoenzymes involved in translation between archaea and eukaryotes

(2018) Nhan van Tran et al.   NUCLEIC ACIDS RESEARCH

Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome

(2018) Sophie S. Abby et al.   Frontiers in Microbiology

The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

(2018) Pakorn Aiewsakun et al.   Microbiome

Phage puppet masters of the marine microbial realm

(2018) Mya Breitbart et al.   Nature Microbiology

Regulation of carbamoylphosphate synthesis in Escherichia coli: an amazing metabolite at the crossroad of arginine and pyrimidine biosynthesis

(2018) Daniel Charlier et al.   AMINO ACIDS

Targeting mechanisms of tailed bacteriophages

(2018) Franklin L. Nobrega et al.   NATURE REVIEWS MICROBIOLOGY

Salmonella Phage S16 Tail Fiber Adhesin Features a Rare Polyglycine Rich Domain for Host Recognition

(2018) Matthew Dunne et al.   STRUCTURE

Characterization of the lytic archaeal virus Drs3 infecting Methanobacterium formicicum

(2018) Sandro Wolf et al.   ARCHIVES OF VIROLOGY

Novel Caudovirales associated with Marine Group I Thaumarchaeota assembled from metagenomes

(2018) Mario López-Pérez et al.   ENVIRONMENTAL MICROBIOLOGY

Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes

(2018) Nathan A. Ahlgren et al.   ISME Journal

Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree

(2018) Guangchuang Yu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Complete Genome Sequence of the Model Halovirus PhiH1 (ΦH1)

(2018) Mike Dyall-Smith et al.   Genes

The enigmatic archaeal virosphere

(2017) David Prangishvili et al.   NATURE REVIEWS MICROBIOLOGY

Putative archaeal viruses from the mesopelagic ocean

(2017) Dean R. Vik et al.   PeerJ

Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean

(2017) Yosuke Nishimura et al.   mSphere

PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data

(2017) Julian R. Garneau et al.   Scientific Reports

Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees

(2016) Kazunori D. Yamada et al.   BIOINFORMATICS

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Dali server update

(2016) Liisa Holm et al.   NUCLEIC ACIDS RESEARCH

The genomic content and context of auxiliary metabolic genes in marine cyanomyoviruses

(2016) Lisa T. Crummett et al.   VIROLOGY

Next-Generation “-omics” Approaches Reveal a Massive Alteration of Host RNA Metabolism during Bacteriophage Infection of Pseudomonas aeruginosa

(2016) Anne Chevallereau et al.   PLoS Genetics

Virus-mediated archaeal hecatomb in the deep seafloor

(2016) R. Danovaro et al.   Science Advances

Haloviruses of archaea, bacteria, and eukaryotes

(2015) Nina S Atanasova et al.   CURRENT OPINION IN MICROBIOLOGY

Analysis of metagenomic data reveals common features of halophilic viral communities across continents

(2015) Simon Roux et al.   ENVIRONMENTAL MICROBIOLOGY

Insights into molecular plasticity in protein complexes from Trm9-Trm112 tRNA modifying enzyme crystal structure

(2015) Juliette Létoquart et al.   NUCLEIC ACIDS RESEARCH

Bacteriophage lambda: Early pioneer and still relevant

(2015) Sherwood R. Casjens et al.   VIROLOGY

Archaeal Viruses Multiply: Temporal Screening in a Solar Saltern

(2015) Nina Atanasova et al.   Viruses-Basel

Biogeography of Viruses in the Sea

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

Archaeal viruses and bacteriophages: comparisons and contrasts

(2014) Maija K. Pietilä et al.   TRENDS IN MICROBIOLOGY

Insights into Head-Tailed Viruses Infecting Extremely Halophilic Archaea

(2013) M. K. Pietila et al.   JOURNAL OF VIROLOGY

Analysis Tool Web Services from the EMBL-EBI

(2013) Hamish McWilliam et al.   NUCLEIC ACIDS RESEARCH

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Structure of the archaeal head-tailed virus HSTV-1 completes the HK97 fold story

(2013) M. K. Pietila et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Snapshot of haloarchaeal tailed virus genomes

(2013) Ana Senčilo et al.   RNA Biology

Phylogenomics of T4 cyanophages: lateral gene transfer in the ‘core’ and origins of host genes

(2012) J. Cesar Ignacio-Espinoza et al.   ENVIRONMENTAL MICROBIOLOGY

Reconstructing Viral Genomes from the Environment Using Fosmid Clones: The Case of Haloviruses

(2012) Inmaculada Garcia-Heredia et al.   PLoS One

A thaumarchaeal provirus testifies for an ancient association of tailed viruses with archaea

(2011) Mart Krupovic et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Easyfig: a genome comparison visualizer

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

Global network of specific virus-host interactions in hypersaline environments

(2011) Nina S. Atanasova et al.   ENVIRONMENTAL MICROBIOLOGY

The gp38 Adhesins of the T4 Superfamily: A Complex Modular Determinant of the Phage’s Host Specificity

(2011) Sabrina N. Trojet et al.   Genome Biology and Evolution

Haloarchaeal myovirus φCh1 harbours a phase variation system for the production of protein variants with distinct cell surface adhesion specificities

(2011) R. Klein et al.   MOLECULAR MICROBIOLOGY

The archaeal cell envelope

(2011) Sonja-Verena Albers et al.   NATURE REVIEWS MICROBIOLOGY

Comparative Analysis of the Mosaic Genomes of Tailed Archaeal Viruses and Proviruses Suggests Common Themes for Virion Architecture and Assembly with Tailed Viruses of Bacteria

(2010) Mart Krupovič et al.   JOURNAL OF MOLECULAR BIOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

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

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

The AAA+ motor complex of subunits CobS and CobT of cobaltochelatase visualized by single particle electron microscopy

(2009) Joakim Lundqvist et al.   JOURNAL OF STRUCTURAL BIOLOGY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

PROMALS3D: a tool for multiple protein sequence and structure alignments

(2008) Jimin Pei et al.   NUCLEIC ACIDS RESEARCH