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

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Application of filamentous phages in environment: A tectonic shift in the science and practice of ecorestoration

(2019) Radhey Shyam Sharma et al.   Ecology and Evolution

Numerous cultivated and uncultivated viruses encode ribosomal proteins

(2019) Carolina M. Mizuno et al.   Nature Communications

Phage-Derived Antibacterials: Harnessing the Simplicity, Plasticity, and Diversity of Phages

(2019) Bi-o Kim et al.   Viruses-Basel

Prophage Hunter: an integrative hunting tool for active prophages

(2019) Wenchen Song 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

Mining, analyzing, and integrating viral signals from metagenomic data

(2019) Tingting Zheng et al.   Microbiome

Missing a Phage: Unraveling Tripartite Symbioses within the Human Gut

(2019) Jeremy J. Barr   mSystems

Nitrogen sourcing during viral infection of marine cyanobacteria

(2019) Jacob R. Waldbauer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning

(2019) Zhencheng Fang et al.   GigaScience

Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease

(2019) Samuel S. Minot et al.   Microbiome

Cryptic prophage-encoded small protein protects Escherichia coli from phage infection by inhibiting inner membrane receptor proteins

(2019) Preethi T. Ragunathan et al.   JOURNAL OF BACTERIOLOGY

Biotechnological applications of bacteriophages: State of the art

(2018) Liliam K. Harada et al.   MICROBIOLOGICAL RESEARCH

Host-linked soil viral ecology along a permafrost thaw gradient

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

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

(2018) Deyvid Amgarten et al.   Frontiers in Genetics

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes

(2018) David Paez-Espino et al.   NUCLEIC ACIDS RESEARCH

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

(2018) Gareth Trubl et al.   mSystems

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Two distinct metacommunities characterize the gut microbiota in Crohn's disease patients

(2017) Qing He et al.   GigaScience

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

(2017) Jie Ren et al.   Microbiome

The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred

(2017) Umer Zeeshan Ijaz et al.   PLoS One

Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

(2017) Michiru Nishita et al.   Scientific Reports

Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer

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

Measurement of bacterial replication rates in microbial communities

(2016) Christopher T Brown et al.   NATURE BIOTECHNOLOGY

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

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

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences

(2016) Nathan A. Ahlgren et al.   NUCLEIC ACIDS RESEARCH

The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences

(2016) Nirav Merchant et al.   PLOS BIOLOGY

Hyperexpansion of RNA Bacteriophage Diversity

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

Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient

(2016) Gareth Trubl et al.   PeerJ

To kill or not to kill: The balance between lytic and lysogenic viral infection is driven by trophic status

(2016) Jérôme P. Payet et al.   LIMNOLOGY AND OCEANOGRAPHY

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

(2015) Jason M. Norman et al.   CELL

The gut microbiome in health and in disease

(2015) Andrew B. Shreiner et al.   CURRENT OPINION IN GASTROENTEROLOGY

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

(2015) Jessica M Labonté et al.   ISME Journal

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

The elemental composition of virus particles: implications for marine biogeochemical cycles

(2014) Luis F. Jover et al.   NATURE REVIEWS MICROBIOLOGY

Sulfur Oxidation Genes in Diverse Deep-Sea Viruses

(2014) K. Anantharaman et al.   SCIENCE

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

(2014) Simon Roux et al.   eLife

Bacteriophage adhering to mucus provide a non-host-derived immunity

(2013) J. J. Barr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

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

(2012) Limin Fu et al.   BIOINFORMATICS

The Impact of the Gut Microbiota on Human Health: An Integrative View

(2012) Jose C. Clemente et al.   CELL

Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes

(2012) D. M. Kristensen et al.   JOURNAL OF BACTERIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

VIROME: a standard operating procedure for analysis of viral metagenome sequences

(2012) K. Eric Wommack et al.   Standards in Genomic Sciences

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Metavir: a web server dedicated to virome analysis

(2011) Simon Roux et al.   BIOINFORMATICS

Easyfig: a genome comparison visualizer

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

Invasive potential of gut mucosa-derived fusobacterium nucleatum positively correlates with IBD status of the host

(2011) Jaclyn Strauss et al.   INFLAMMATORY BOWEL DISEASES

Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism

(2011) L. R. Thompson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean

(2010) Kimberly P Tucker et al.   ISME Journal

Viral Mutation Rates

(2010) R. Sanjuan et al.   JOURNAL OF VIROLOGY

Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean

(2010) Nianzhi Jiao et al.   NATURE REVIEWS MICROBIOLOGY

Global-scale processes with a nanoscale drive: the role of marine viruses

(2008) Corina P D Brussaard et al.   ISME Journal

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

(2008) D. A. Rasko et al.   JOURNAL OF BACTERIOLOGY

Modeling the Fitness Consequences of a Cyanophage-Encoded Photosynthesis Gene

(2008) Jason G. Bragg et al.   PLoS One