Uncovering Earth’s virome

Microbiome Data Science: Understanding Our Microbial Planet

(2016) Nikos C. Kyrpides et al.   TRENDS IN MICROBIOLOGY

Membrane biofouling in a wastewater nitrification reactor: Microbial succession from autotrophic colonization to heterotrophic domination

(2016) Huijie Lu et al.   WATER RESEARCH

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

(2016) Nirav Merchant et al.   PLOS BIOLOGY

The isolation and characterization of two Stenotrophomonas maltophilia bacteriophages capable of cross-taxonomic order infectivity

(2015) Danielle L. Peters et al.   BMC GENOMICS

Global transcription of CRISPR loci in the human oral cavity

(2015) Andrew G Lum et al.   BMC GENOMICS

Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation

(2015) Bernhard Tschitschko et al.   ISME Journal

Global diversity and biogeography of deep-sea pelagic prokaryotes

(2015) Guillem Salazar et al.   ISME Journal

Methods for virus classification and the challenge of incorporating metagenomic sequence data

(2015) Peter Simmonds   JOURNAL OF GENERAL VIROLOGY

A century of the phage: past, present and future

(2015) George P. C. Salmond et al.   NATURE REVIEWS MICROBIOLOGY

Rising to the challenge: accelerated pace of discovery transforms marine virology

(2015) Jennifer R. Brum et al.   NATURE REVIEWS MICROBIOLOGY

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

Programming Bacteriophages by Swapping Their Specificity Determinants

(2015) Moran G. Goren et al.   TRENDS IN MICROBIOLOGY

Large-scale contamination of microbial isolate genomes by Illumina PhiX control

(2015) Supratim Mukherjee et al.   Standards in Genomic Sciences

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

(2015) Marcel Huntemann et al.   Standards in Genomic Sciences

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Biogeography of Viruses in the Sea

(2015) Cheryl-Emiliane T. Chow et al.   Annual Review of Virology

Metagenomic analysis of double-stranded DNA viruses in healthy adults

(2014) Kristine M Wylie et al.   BMC BIOLOGY

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

(2014) Bonnie L Hurwitz et al.   ISME Journal

When a virus is not a parasite: the beneficial effects of prophages on bacterial fitness

(2014) Joseph Bondy-Denomy et al.   JOURNAL OF MICROBIOLOGY

Molecular Bases and Role of Viruses in the Human Microbiome

(2014) Shira R. Abeles et al.   JOURNAL OF MOLECULAR BIOLOGY

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

(2014) T.B.K. Reddy et al.   NUCLEIC ACIDS RESEARCH

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

Association between living environment and human oral viral ecology

(2013) Refugio Robles-Sikisaka et al.   ISME Journal

IMG/M 4 version of the integrated metagenome comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia

(2013) Joanne B. Emerson et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

The global virome: not as big as we thought?

(2013) J Cesar Ignacio-Espinoza et al.   Current Opinion in Virology

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

A call for standardized classification of metagenome projects

(2010) Natalia Ivanova et al.   ENVIRONMENTAL MICROBIOLOGY

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Short motif sequences determine the targets of the prokaryotic CRISPR defence system

(2009)   MICROBIOLOGY-SGM

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE

Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities

(2008) A. F. Andersson et al.   SCIENCE