Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation

Interaction dynamics and virus–host range for estuarine actinophages captured by epicPCR

(2021) Eric G. Sakowski et al.   Nature Microbiology

The advantages of the Matthews correlation coefficient (MCC) over F1 score and accuracy in binary classification evaluation

(2020) Davide Chicco et al.   BMC GENOMICS

Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column

(2020) Elaine Luo et al.   ISME Journal

Phage-specific metabolic reprogramming of virocells

(2020) Cristina Howard-Varona et al.   ISME Journal

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

(2020) J. Callanan et al.   Science Advances

DRAM for distilling microbial metabolism to automate the curation of microbiome function

(2020) Michael Shaffer et al.   NUCLEIC ACIDS RESEARCH

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

(2020) Kristopher Kieft et al.   Microbiome

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

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

Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline

(2020) Paraskevi Mara et al.   ISME Journal

Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

(2020) M. Consuelo Gazitúa et al.   ISME Journal

Viral species richness and composition in young children with loose or watery stool in Ethiopia

(2019) Kristen Aiemjoy et al.   BMC INFECTIOUS DISEASES

Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism

(2019) Disa Bäckström et al.   mBio

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

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

The Promises and Pitfalls of Machine Learning for Detecting Viruses in Aquatic Metagenomes

(2019) Alise J. Ponsero et al.   Frontiers in Microbiology

Diversities and potential biogeochemical impacts of mangrove soil viruses

(2019) Min Jin et al.   Microbiome

Mining, analyzing, and integrating viral signals from metagenomic data

(2019) Tingting Zheng et al.   Microbiome

Detecting contamination in viromes using ViromeQC

(2019) Moreno Zolfo et al.   NATURE BIOTECHNOLOGY

Single-Stranded DNA Viruses in Antarctic Cryoconite Holes

(2019) Pacifica Sommers et al.   Viruses-Basel

Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease

(2019) Adam G. Clooney et al.   Cell Host & Microbe

Prokaryotic Population Dynamics and Viral Predation in a Marine Succession Experiment Using Metagenomics

(2019) Jose M. Haro-Moreno et al.   Frontiers in Microbiology

Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation

(2019) Eitan Yaffe et al.   Nature Microbiology

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

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

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Coccolithovirus facilitation of carbon export in the North Atlantic

(2018) Christien P. Laber et al.   Nature Microbiology

Phage puppet masters of the marine microbial realm

(2018) Mya Breitbart et al.   Nature Microbiology

Host-linked soil viral ecology along a permafrost thaw gradient

(2018) Joanne B. Emerson et al.   Nature Microbiology

Enteric Virome and Bacterial Microbiota in Children with Ulcerative Colitis and Crohnʼs Disease

(2018) Melissa A. Fernandes et al.   JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION

MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins

(2018) Deyvid Amgarten et al.   Frontiers in Genetics

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

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

T4-type viruses: Important impacts on shaping bacterial community along a chronosequence of 2000-year old paddy soils

(2018) Yong Li et al.   SOIL BIOLOGY & BIOCHEMISTRY

Adaptation to sub-optimal hosts is a driver of viral diversification in the ocean

(2018) Hagay Enav et al.   Nature Communications

Cyanophage-encoded lipid desaturases: oceanic distribution, diversity and function

(2017) Sheila Roitman et al.   ISME Journal

Namib Desert Soil Microbial Community Diversity, Assembly, and Function Along a Natural Xeric Gradient

(2017) Vincent Scola et al.   MICROBIAL ECOLOGY

Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data

(2017) David Paez-Espino et al.   Nature Protocols

Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans

(2017) Felipe H. Coutinho et al.   Nature Communications

Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics

(2017) Mohammad Moniruzzaman et al.   Nature Communications

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

(2017) Simon Roux et al.   PeerJ

Unveiling the role and life strategies of viruses from the surface to the dark ocean

(2017) Elena Lara et al.   Science Advances

Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer

(2016) Ann C. Gregory et al.   BMC GENOMICS

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

(2016) François Enault et al.   ISME Journal

Plankton networks driving carbon export in the oligotrophic ocean

(2016) Lionel Guidi et al.   NATURE

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

Virocell Metabolism: Metabolic Innovations During Host–Virus Interactions in the Ocean

(2016) Shilo Rosenwasser et al.   TRENDS IN MICROBIOLOGY

HostPhinder: A Phage Host Prediction Tool

(2016) Julia Villarroel et al.   Viruses-Basel

MetaPhinder—Identifying Bacteriophage Sequences in Metagenomic Data Sets

(2016) Vanessa Isabell Jurtz et al.   PLoS One

Diversity and Ecology of Viruses in Hyperarid Desert Soils

(2015) Olivier Zablocki et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2015) Jason M. Norman et al.   CELL

Counts and sequences, observations that continue to change our understanding of viruses in nature

(2015) K. Eri Wommack et al.   JOURNAL OF MICROBIOLOGY

Early life dynamics of the human gut virome and bacterial microbiome in infants

(2015) Efrem S Lim et al.   NATURE MEDICINE

I-TASSER server: new development for protein structure and function predictions

(2015) Jianyi Yang et al.   NUCLEIC ACIDS RESEARCH

Gut DNA viromes of Malawian twins discordant for severe acute malnutrition

(2015) Alejandro Reyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis

(2015) Nádia Conceição-Neto et al.   Scientific Reports

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Metagenomic analysis of the viral community in Namib Desert hypoliths

(2014) Evelien M. Adriaenssens et al.   ENVIRONMENTAL MICROBIOLOGY

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

(2014) Bonnie L Hurwitz et al.   ISME Journal

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

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

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

(2014) Li Deng et al.   NATURE

Sulfur Oxidation Genes in Diverse Deep-Sea Viruses

(2014) K. Anantharaman et al.   SCIENCE

Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences

(2013) S. Roux et al.   Open Biology

Expanding the Marine Virosphere Using Metagenomics

(2013) Carolina Megumi Mizuno et al.   PLoS Genetics

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

The automatic annotation of bacterial genomes

(2012) E. J. Richardson et al.   BRIEFINGS IN BIOINFORMATICS

Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics

(2012) Bonnie L. Hurwitz et al.   ENVIRONMENTAL MICROBIOLOGY

Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method

(2012) Melissa B. Duhaime et al.   ENVIRONMENTAL MICROBIOLOGY

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

New and continuing developments at PROSITE

(2012) Christian J. A. Sigrist et al.   NUCLEIC ACIDS RESEARCH

Easyfig: a genome comparison visualizer

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

Second Internal Thoracic Artery Versus Radial Artery in Coronary Artery Bypass Grafting

(2011) Elfriede Ruttmann et al.   CIRCULATION

Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments

(2010) Matthew B. Sullivan et al.   ENVIRONMENTAL MICROBIOLOGY

Multiple displacement amplification compromises quantitative analysis of metagenomes

(2010) Suzan Yilmaz et al.   NATURE METHODS

A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment

(2009) Shani Tzahor et al.   BMC GENOMICS

Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence ofSynechococcushost genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution

(2009) Andrew D. Millard et al.   ENVIRONMENTAL MICROBIOLOGY

Efficient Phage-Mediated Pigment Biosynthesis in Oceanic Cyanobacteria

(2008) Thorben Dammeyer et al.   CURRENT BIOLOGY

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE