IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata

Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes

(2023) Matthew M. Carter et al.   CELL

Plasmid classifications

(2023) M. Pilar Garcillán-Barcia et al.   PLASMID

Identification of mobile genetic elements with geNomad

(2023) Antonio Pedro Camargo et al.   NATURE BIOTECHNOLOGY

Petabase-scale sequence alignment catalyses viral discovery

(2022) Robert C. Edgar et al.   NATURE

Metagenomic assembled plasmids of the human microbiome vary across disease cohorts

(2022) S. R. Stockdale et al.   Scientific Reports

A plasmid network from the gut microbiome of semi-isolated human groups reveals unique and shared metabolic and virulence traits

(2022) Liliane Costa Conteville et al.   Scientific Reports

GTDB-Tk v2: memory friendly classification with the genome taxonomy database

(2022) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

Expansion of the global RNA virome reveals diverse clades of bacteriophages

(2022) Uri Neri et al.   CELL

Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9

(2022) Supratim Mukherjee et al.   NUCLEIC ACIDS RESEARCH

Selfish, promiscuous and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations

(2022) Matthieu Haudiquet et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata

(2022) Antonio Pedro Camargo et al.   NUCLEIC ACIDS RESEARCH

The IMG/M data management and analysis system v.7: content updates and new features

(2022) I-Min A Chen et al.   NUCLEIC ACIDS RESEARCH

Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation

(2022) Manuel Ares-Arroyo et al.   NUCLEIC ACIDS RESEARCH

Beyond horizontal gene transfer: the role of plasmids in bacterial evolution

(2021) Jerónimo Rodríguez-Beltrán et al.   NATURE REVIEWS MICROBIOLOGY

Sensitive protein alignments at tree-of-life scale using DIAMOND

(2021) Benjamin Buchfink et al.   NATURE METHODS

DOE JGI Metagenome Workflow

(2021) Alicia Clum et al.   mSystems

COPLA, a taxonomic classifier of plasmids

(2021) Santiago Redondo-Salvo et al.   BMC BIOINFORMATICS

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

(2021) Donovan H Parks et al.   NUCLEIC ACIDS RESEARCH

PLSDB: advancing a comprehensive database of bacterial plasmids

(2021) Georges P Schmartz et al.   NUCLEIC ACIDS RESEARCH

Giant virus diversity and host interactions through global metagenomics

(2020) Frederik Schulz et al.   NATURE

A complete domain-to-species taxonomy for Bacteria and Archaea

(2020) Donovan H. Parks et al.   NATURE BIOTECHNOLOGY

Analysis of COMPASS, a New Comprehensive Plasmid Database Revealed Prevalence of Multireplicon and Extensive Diversity of IncF Plasmids

(2020) Pierre-Emmanuel Douarre et al.   Frontiers in Microbiology

A unified catalog of 204,938 reference genomes from the human gut microbiome

(2020) Alexandre Almeida et al.   NATURE BIOTECHNOLOGY

Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids

(2020) Santiago Redondo-Salvo et al.   Nature Communications

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

(2019) Edoardo Pasolli et al.   CELL

Plasmid detection and assembly in genomic and metagenomic datasets

(2019) Dmitry Antipov et al.   GENOME RESEARCH

Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes

(2019) Simon Roux et al.   Nature Microbiology

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Evolution of Plasmid-Mediated Antibiotic Resistance in the Clinical Context

(2018) Alvaro San Millan   TRENDS IN MICROBIOLOGY

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

(2018) Tiago F Jesus et al.   NUCLEIC ACIDS RESEARCH

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

GenBank

(2016) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

Hundreds of Circular Novel Plasmids and DNA Elements Identified in a Rat Cecum Metamobilome

(2014) Tue Sparholt Jørgensen et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS