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August 2003 |
DRAM for distilling microbial metabolism to automate the curation of microbiome function
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August 2020 |
Sulfur Oxidation Genes in Diverse Deep-Sea Viruses
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May 2014 |
Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence of Synechococcus host genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution
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September 2009 |
Host-linked soil viral ecology along a permafrost thaw gradient
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July 2018 |
Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome
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August 2014 |
The advantages of the Matthews correlation coefficient (MCC) over F1 score and accuracy in binary classification evaluation
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January 2020 |
Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method: Linker amplification for ultra-low DNA samples
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June 2012 |
A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core
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July 2018 |
Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data
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July 2017 |
PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes
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September 2017 |
Metagenomic analysis of the viral community in Namib Desert hypoliths: Metaviromics of Namib hypoliths
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July 2014 |
Marine DNA Viral Macro- and Microdiversity from Pole to Pole
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May 2019 |
Viral tagging reveals discrete populations in Synechococcus viral genome sequence space
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July 2014 |
Genomic variation landscape of the human gut microbiome
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December 2012 |
Computational approaches to predict bacteriophage–host relationships
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December 2015 |
VirSorter: mining viral signal from microbial genomic data
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January 2015 |
Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments: Comparative genomics of T4-like myoviruses
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November 2010 |
Exploring the Vast Diversity of Marine Viruses
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June 2007 |
Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution
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September 2007 |
Second Internal Thoracic Artery Versus Radial Artery in Coronary Artery Bypass Grafting: A Long-Term, Propensity Score–Matched Follow-Up Study
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September 2011 |
Photosynthesis genes in marine viruses yield proteins during host infection
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October 2005 |
Mining, analyzing, and integrating viral signals from metagenomic data
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March 2019 |
Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics: Viral community concentration and purification
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July 2012 |
A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment
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January 2009 |
Phage-specific metabolic reprogramming of virocells
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January 2020 |
Uncovering Earth’s virome
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August 2016 |
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
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July 2002 |
Single-Stranded DNA Viruses in Antarctic Cryoconite Holes
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November 2019 |
MetaPhinder—Identifying Bacteriophage Sequences in Metagenomic Data Sets
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September 2016 |
RNAMotif, an RNA secondary structure definition and search algorithm
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November 2001 |
Gut DNA viromes of Malawian twins discordant for severe acute malnutrition
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September 2015 |
Coccolithovirus facilitation of carbon export in the North Atlantic
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March 2018 |
Enteric Virome and Bacterial Microbiota in Children With Ulcerative Colitis and Crohn Disease
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January 2019 |
Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen
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January 2001 |
WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs
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July 2017 |
Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline
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August 2020 |
ViPTree: the viral proteomic tree server
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March 2017 |
Efficient Phage-Mediated Pigment Biosynthesis in Oceanic Cyanobacteria
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March 2008 |
The automatic annotation of bacterial genomes
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March 2012 |
The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut
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November 2020 |
Transcription of a 'photosynthetic' T4-type phage during infection of a marine cyanobacterium
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May 2006 |
SWISS-MODEL: homology modelling of protein structures and complexes
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journal
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May 2018 |
Interactive Tree Of Life (iTOL) v4: recent updates and new developments
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April 2019 |
Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses
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June 2016 |
Plankton networks driving carbon export in the oligotrophic ocean
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February 2016 |
Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans
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July 2017 |
RDP4: Detection and analysis of recombination patterns in virus genomes
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March 2015 |
Expanding the Marine Virosphere Using Metagenomics
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December 2013 |
Unveiling the role and life strategies of viruses from the surface to the dark ocean
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September 2017 |
A network-based integrated framework for predicting virus–prokaryote interactions
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June 2020 |
T4-type viruses: Important impacts on shaping bacterial community along a chronosequence of 2000-year old paddy soils
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January 2019 |
Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences
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December 2013 |
Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
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January 2017 |
Summary for Policymakers
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book
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March 2014 |
I-TASSER server: new development for protein structure and function predictions
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journal
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April 2015 |
Detecting contamination in viromes using ViromeQC
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November 2019 |
Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
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May 2019 |
Viral photosynthetic reaction center genes and transcripts in the marine environment
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journal
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August 2007 |
Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes
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October 2018 |
Phage puppet masters of the marine microbial realm
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June 2018 |
Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer
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November 2016 |
Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters
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November 2020 |
Expansion of known ssRNA phage genomes: From tens to over a thousand
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February 2020 |
Viral species richness and composition in young children with loose or watery stool in Ethiopia
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January 2019 |
Counts and sequences, observations that continue to change our understanding of viruses in nature
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March 2015 |
Early life dynamics of the human gut virome and bacterial microbiome in infants
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September 2015 |
Adaptation to sub-optimal hosts is a driver of viral diversification in the ocean
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November 2018 |
Patterns and ecological drivers of ocean viral communities
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May 2015 |
The Promises and Pitfalls of Machine Learning for Detecting Viruses in Aquatic Metagenomes
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April 2019 |
Diversity and Ecology of Viruses in Hyperarid Desert Soils
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November 2015 |
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses
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September 2016 |
Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis
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November 2015 |
Easyfig: a genome comparison visualizer
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January 2011 |
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation
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journal
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August 2019 |
Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease
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December 2019 |
Metabolic reprogramming by viruses in the sunlit and dark ocean
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journal
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January 2013 |
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
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November 2014 |
Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts
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journal
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July 2006 |
Diversities and potential biogeochemical impacts of mangrove soil viruses
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journal
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April 2019 |
Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics
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journal
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June 2017 |
Namib Desert Soil Microbial Community Diversity, Assembly, and Function Along a Natural Xeric Gradient
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journal
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June 2017 |
Functional metagenomic profiling of nine biomes
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journal
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March 2008 |
Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease
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journal
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January 2015 |
VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences
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journal
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June 2020 |
HostPhinder: A Phage Host Prediction Tool
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journal
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May 2016 |
Multiple displacement amplification compromises quantitative analysis of metagenomes
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journal
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November 2010 |
Identifying viruses from metagenomic data using deep learning
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journal
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January 2020 |
MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins
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journal
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August 2018 |
Virocell Metabolism: Metabolic Innovations During Host–Virus Interactions in the Ocean
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journal
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October 2016 |
VIRIDIC—A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses
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journal
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November 2020 |
Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column
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journal
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February 2020 |
Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation
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journal
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December 2019 |
Prokaryotic Population Dynamics and Viral Predation in a Marine Succession Experiment Using Metagenomics
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journal
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December 2019 |
Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake
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journal
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January 2007 |
Interaction dynamics and virus–host range for estuarine actinophages captured by epicPCR
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journal
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February 2021 |
Marine viruses and their biogeochemical and ecological effects
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journal
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June 1999 |
New and continuing developments at PROSITE
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journal
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November 2012 |
Cyanophage-encoded lipid desaturases: oceanic distribution, diversity and function
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journal
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October 2017 |