mMGE: a database for human metagenomic extrachromosomal mobile genetic elements

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

(2020) Kristopher Kieft et al.   Microbiome

Virulence factors, prevalence and potential transmission of extraintestinal pathogenic Escherichia coli isolated from different sources: recent reports

(2019) Jolanta Sarowska et al.   Gut Pathogens

Bacteriophages as Environmental Reservoirs of Antibiotic Resistance

(2019) William Calero-Cáceres et al.   TRENDS IN MICROBIOLOGY

Plasmid detection and assembly in genomic and metagenomic datasets

(2019) Dmitry Antipov et al.   GENOME RESEARCH

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

Phages and Human Health: More Than Idle Hitchhikers

(2019) Lawrence et al.   Viruses-Basel

Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance

(2019) Tanita Wein et al.   Nature Communications

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

(2019) Zhencheng Fang et al.   GigaScience

Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut

(2019) Yoshihiko Suzuki et al.   Microbiome

The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific

(2019) Andrey N. Shkoporov et al.   Cell Host & Microbe

Detecting contamination in viromes using ViromeQC

(2019) Moreno Zolfo et al.   NATURE BIOTECHNOLOGY

OUP accepted manuscript

(2018)   BIOINFORMATICS

Alterations in Enteric Virome Are Associated With Colorectal Cancer and Survival Outcomes

(2018) Geicho Nakatsu et al.   GASTROENTEROLOGY

Lineage-specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group

(2018) Guillaume Méric et al.   MOLECULAR ECOLOGY

Clustering huge protein sequence sets in linear time

(2018) Martin Steinegger et al.   Nature Communications

Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities

(2018) Ramakrishnan Sitaraman   Microbiome

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data

(2018) Tiago F Jesus 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

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data

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

MVP: a microbe–phage interaction database

(2017) Na L Gao et al.   NUCLEIC ACIDS RESEARCH

Persistence and reversal of plasmid-mediated antibiotic resistance

(2017) Allison J. Lopatkin et al.   Nature Communications

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients

(2017) J. R. Bedarf et al.   Genome Medicine

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

(2017) Simon Roux et al.   PeerJ

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

(2017) Jie Ren et al.   Microbiome

Acquisition of virulence factors in livestock-associated MRSA: Lysogenic conversion of CC398 strains by virulence gene-containing phages

(2017) Britta Kraushaar et al.   Scientific Reports

Viral metabolic reprogramming in marine ecosystems

(2016) Bonnie L Hurwitz et al.   CURRENT OPINION IN MICROBIOLOGY

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

(2016) Dinghua Li et al.   METHODS

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

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

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

Temperate phages both mediate and drive adaptive evolution in pathogen biofilms

(2016) Emily V. Davies et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) Shilo Rosenwasser et al.   TRENDS IN MICROBIOLOGY

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

(2015) Jason M. Norman et al.   CELL

The Pfam protein families database: towards a more sustainable future

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

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

(2015) Simon Roux et al.   eLife

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Using MeSH (Medical Subject Headings) to Enhance PubMed Search Strategies for Evidence-Based Practice in Physical Therapy

(2011) R. R. Richter et al.   PHYSICAL THERAPY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

ACLAME: A CLAssification of Mobile genetic Elements, update 2010

(2009) Raphaël Leplae et al.   NUCLEIC ACIDS RESEARCH

The Universal Protein Resource (UniProt) in 2010

(2009)   NUCLEIC ACIDS RESEARCH