RNA viromes from terrestrial sites across China expand environmental viral diversity

Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome

(2022) Ahmed A. Zayed et al.   SCIENCE

A new coronavirus associated with human respiratory disease in China

(2020) Fan Wu et al.   NATURE

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

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

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

SignalP 5.0 improves signal peptide predictions using deep neural networks

(2019) José Juan Almagro Armenteros et al.   NATURE BIOTECHNOLOGY

Diversities and potential biogeochemical impacts of mangrove soil viruses

(2019) Min Jin et al.   Microbiome

Identification and genetic characterization of a porcine hepe-astrovirus (bastrovirus) in the United States

(2019) Fernando V. Bauermann et al.   ARCHIVES OF VIROLOGY

Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

(2019) Evan P. Starr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Using Metagenomics to Characterize an Expanding Virosphere

(2018) Yong-Zhen Zhang et al.   CELL

Decreasing soil microbial diversity is associated with decreasing microbial biomass under nitrogen addition

(2018) Chao Wang et al.   SOIL BIOLOGY & BIOCHEMISTRY

Meta-transcriptomics and the evolutionary biology of RNA viruses

(2018) Mang Shi et al.   VIRUS RESEARCH

Effects of Nitrogen and Phosphorus Inputs on Soil Bacterial Abundance, Diversity, and Community Composition in Chinese Fir Plantations

(2018) Qing Wang et al.   Frontiers in Microbiology

Origins and Evolution of the Global RNA Virome

(2018) Yuri I. Wolf et al.   mBio

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

(2018) Gareth Trubl et al.   mSystems

Virus taxonomy in the age of metagenomics

(2017) Peter Simmonds et al.   NATURE REVIEWS MICROBIOLOGY

Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons

(2017) Ilias Lagkouvardos et al.   PeerJ

FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance

(2016) Syun-ichi Urayama et al.   MICROBES AND ENVIRONMENTS

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

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

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

(2015) Dinghua Li et al.   BIOINFORMATICS

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

(2015) Ci-Xiu Li et al.   eLife

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

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

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Estimates of viral abundance in soils are strongly influenced by extraction and enumeration methods

(2013) Kurt E. Williamson et al.   BIOLOGY AND FERTILITY OF SOILS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Are we missing half of the viruses in the ocean?

(2012) Grieg F Steward et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

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

(2011) Michael Remmert et al.   NATURE METHODS

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

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

The life of diatoms in the world's oceans

(2009) E. Virginia Armbrust   NATURE