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

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

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

(2019) Jakub Barylski et al.   SYSTEMATIC BIOLOGY

Changes to virus taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2019)

(2019) Peter J. Walker et al.   ARCHIVES OF VIROLOGY

Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes

(2019) Simon Roux et al.   Nature Microbiology

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

(2019) Robert A. Edwards et al.   Nature Microbiology

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

(2018) Lukas Zimmermann et al.   JOURNAL OF MOLECULAR BIOLOGY

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Geospatial distribution of viromes in tropical freshwater ecosystems

(2018) Xiaoqiong Gu et al.   WATER RESEARCH

RNA-dependent RNA targeting by CRISPR-Cas9

(2018) Steven C Strutt et al.   eLife

Origins and Evolution of the Global RNA Virome

(2018) Yuri I. Wolf et al.   mBio

Freshwater carbon and nutrient cycles revealed through reconstructed population genomes

(2018) Alexandra M. Linz et al.   PeerJ

Giant viruses with an expanded complement of translation system components

(2017) Frederik Schulz et al.   SCIENCE

On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires

(2017) Sukrit Silas et al.   mBio

Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay

(2017) Martial Marbouty et al.   Science Advances

In situ structures of the genome and genome-delivery apparatus in a single-stranded RNA virus

(2016) Xinghong Dai et al.   NATURE

Redefining the invertebrate RNA virosphere

(2016) Mang Shi et al.   NATURE

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

(2016) Ana Laura Grazziotin et al.   NUCLEIC ACIDS RESEARCH

Asymmetric cryo-EM structure of the canonicalAllolevivirusQβ reveals a single maturation protein and the genomic ssRNA in situ

(2016) Karl V. Gorzelnik et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Healthy human gut phageome

(2016) Pilar Manrique et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hyperexpansion of RNA Bacteriophage Diversity

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

Viruses as Winners in the Game of Life

(2016) Ana Georgina Cobián Güemes et al.   Annual Review of Virology

Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity

(2016) Ran Mei et al.   Scientific Reports

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

(2015) Manuel Kleiner et al.   BMC GENOMICS

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

(2015) Jason M. Norman et al.   CELL

Structural basis for RNA-genome recognition during bacteriophage Qβ replication

(2015) Heidi Gytz et al.   NUCLEIC ACIDS RESEARCH

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data

(2014) Adriana Alberti et al.   BMC GENOMICS

Experimental Approaches for Defining Functional Roles of Microbes in the Human Gut

(2013) Gautam Dantas et al.   Annual Review of Microbiology

Diversity of pili-specific bacteriophages: genome sequence of IncM plasmid-dependent RNA phage M

(2012) Janis Rumnieks et al.   BMC MICROBIOLOGY

Rethinking the Evolution of Single-Stranded RNA (ssRNA) Bacteriophages Based on Genomic Sequences and Characterizations of Two R-Plasmid-Dependent ssRNA Phages, C-1 and Hgal1

(2012) Sherin Kannoly et al.   JOURNAL OF BACTERIOLOGY

Genome Structure of Caulobacter Phage phiCb5

(2011) A. Kazaks et al.   JOURNAL OF VIROLOGY

Why do RNA viruses recombine?

(2011) Etienne Simon-Loriere et al.   NATURE REVIEWS MICROBIOLOGY

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Bacteriophages and their genomes

(2011) Graham F Hatfull et al.   Current Opinion in Virology

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS