Petabase-scale sequence alignment catalyses viral discovery

Diversification of mammalian deltaviruses by host shifting

(2021) Laura M. Bergner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of novel avian and mammalian deltaviruses provides new insights into deltavirus evolution

(2021) Masashi Iwamoto et al.   Virus Evolution

Massive expansion of human gut bacteriophage diversity

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

Sensitive protein alignments at tree-of-life scale using DIAMOND

(2021) Benjamin Buchfink et al.   NATURE METHODS

coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies

(2021) Dmitry Meleshko et al.   BIOINFORMATICS

Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae

(2021) Allison K Miller et al.   Virus Evolution

BioSamples database: FAIRer samples metadata to accelerate research data management

(2021) Mélanie Courtot et al.   NUCLEIC ACIDS RESEARCH

Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data

(2020) Lucas Czech et al.   BIOINFORMATICS

Global Organization and Proposed Megataxonomy of the Virus World

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

Clades of huge phages from across Earth’s ecosystems

(2020) Basem Al-Shayeb et al.   NATURE

Midkine is a dual regulator of wound epidermis development and inflammation during the initiation of limb regeneration

(2020) Stephanie L Tsai et al.   eLife

Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses

(2020) Michael Letko et al.   Nature Microbiology

Rapid Reconstitution of the Faecal Microbiome after Extended Diet-Induced Changes Indicate a Stable Gut Microbiome in Healthy Adult Dogs

(2020) David Allaway et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

VADR: validation and annotation of virus sequence submissions to GenBank

(2020) Alejandro A. Schäffer et al.   BMC BIOINFORMATICS

Global shifts in mammalian population trends reveal key predictors of virus spillover risk

(2020) Christine K. Johnson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Snake Deltavirus Utilizes Envelope Proteins of Different Viruses To Generate Infectious Particles

(2020) Leonora Szirovicza et al.   mBio

An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes

(2020) Lamia Wahba et al.   mSphere

Metaviral SPAdes: assembly of viruses from metagenomic data

(2020) Dmitry Antipov et al.   BIOINFORMATICS

Ecosystem decay exacerbates biodiversity loss with habitat loss

(2020) Jonathan M. Chase et al.   NATURE

Bat-borne virus diversity, spillover and emergence

(2020) Michael Letko et al.   NATURE REVIEWS MICROBIOLOGY

Mammalian deltavirus without hepadnavirus coinfection in the neotropical rodentProechimys semispinosus

(2020) Sofia Paraskevopoulou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Infection by Hepatitis Delta Virus

(2020) John M. Taylor   Viruses-Basel

No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics

(2020) Dannon Baker et al.   PLoS Pathogens

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

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Megaphages infect Prevotella and variants are widespread in gut microbiomes

(2019) Audra E. Devoto et al.   Nature Microbiology

Ultrafast search of all deposited bacterial and viral genomic data

(2019) Phelim Bradley et al.   NATURE BIOTECHNOLOGY

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs

(2019) Dmitry Meleshko et al.   GENOME RESEARCH

ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models

(2019) Diego Darriba et al.   MOLECULAR BIOLOGY AND EVOLUTION

Endangered wild salmon infected by newly discovered viruses

(2019) Gideon J Mordecai et al.   eLife

rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data

(2019) Elena Bushmanova et al.   GigaScience

Parallelization of MAFFT for large-scale multiple sequence alignments

(2018) Tsukasa Nakamura et al.   BIOINFORMATICS

The evolutionary history of vertebrate RNA viruses

(2018) Mang Shi et al.   NATURE

Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

(2018) F. Lemoine et al.   NATURE

The Global Virome Project

(2018) Dennis Carroll et al.   SCIENCE

Description and initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new family Abyssoviridae, and from a sister group to the Coronavirinae, the proposed genus Alphaletovirus

(2018) Khulud Bukhari et al.   VIROLOGY

ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes

(2018) Benoit Morel et al.   BIOINFORMATICS

A Divergent Hepatitis D-Like Agent in Birds

(2018) Michelle Wille et al.   Viruses-Basel

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Database resources of the National Center for Biotechnology Information

(2017) et al.   NUCLEIC ACIDS RESEARCH

The global burden of viral hepatitis from 1990 to 2013: findings from the Global Burden of Disease Study 2013

(2016) Jeffrey D Stanaway et al.   LANCET

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

IVA: accuratede novoassembly of RNA virus genomes

(2015) Martin Hunt et al.   BIOINFORMATICS

Viroids: Survivors from the RNA World?

(2014) Ricardo Flores et al.   Annual Review of Microbiology

Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements

(2014) Eugene V. Koonin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

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

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

A systematic comparison of the MetaCyc and KEGG pathway databases

(2013) Tomer Altman et al.   BMC BIOINFORMATICS

A Strategy To Estimate Unknown Viral Diversity in Mammals

(2013) S. J. Anthony et al.   mBio

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

Ultrafast clustering algorithms for metagenomic sequence analysis

(2012) W. Li et al.   BRIEFINGS IN BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The Sensitivity of Massively Parallel Sequencing for Detecting Candidate Infectious Agents Associated with Human Tissue

(2011) Richard A. Moore et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

CloudBurst: highly sensitive read mapping with MapReduce

(2009) M. C. Schatz   BIOINFORMATICS

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

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS