A Peek into the Plasmidome of Global Sewage

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

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

Abundance and diversity of resistomes differ between healthy human oral cavities and gut

(2020) Victoria R. Carr et al.   Nature Communications

The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography

(2020) Tayte P. Campbell et al.   ISME Journal

Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing

(2019) You Che et al.   Microbiome

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

(2019) Rene S. Hendriksen et al.   Nature Communications

Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes

(2019) Ankita Kothari et al.   mBio

Antibiotic Resistomes in Plant Microbiomes

(2019) Qing-Lin Chen et al.   TRENDS IN PLANT SCIENCE

Plasmid detection and assembly in genomic and metagenomic datasets

(2019) Dmitry Antipov et al.   GENOME RESEARCH

Linking the resistome and plasmidome to the microbiome

(2019) Thibault Stalder et al.   ISME Journal

Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes

(2019) Denis Bertrand et al.   NATURE BIOTECHNOLOGY

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

(2019) Brian P Alcock et al.   NUCLEIC ACIDS RESEARCH

Unravelling plasmidome distribution and interaction with its hosting microbiome

(2019) Aya Brown Kav et al.   ENVIRONMENTAL MICROBIOLOGY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Circular DNA elements of chromosomal origin are common in healthy human somatic tissue

(2018) Henrik Devitt Møller et al.   Nature Communications

Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries

(2018) Patrick Munk et al.   Nature Microbiology

Rapid and precise alignment of raw reads against redundant databases with KMA

(2018) Philip T. L. C. Clausen et al.   BMC BIOINFORMATICS

Evolution of Plasmid-Mediated Antibiotic Resistance in the Clinical Context

(2018) Alvaro San Millan   TRENDS IN MICROBIOLOGY

The Pfam protein families database in 2019

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

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

MCR-1-producing Klebsiella pneumoniae outbreak in China

(2017) Guo-Bao Tian et al.   LANCET INFECTIOUS DISEASES

Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding

(2017) Freeman Lan et al.   NATURE BIOTECHNOLOGY

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants

(2017) Sophie Lanciano et al.   PLoS Genetics

Recycler: an algorithm for detecting plasmids fromde novoassembly graphs

(2016) Roye Rozov et al.   BIOINFORMATICS

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

(2016) Heng Li   BIOINFORMATICS

plasmidSPAdes: assembling plasmids from whole genome sequencing data

(2016) Dmitry Antipov et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Bacterial phylogeny structures soil resistomes across habitats

(2014) Kevin J. Forsberg et al.   NATURE

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Community-wide plasmid gene mobilization and selection

(2013) Vladimir Sentchilo et al.   ISME Journal

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Insights into the bovine rumen plasmidome

(2012) A. B. Kav et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extrachromosomal MicroDNAs and Chromosomal Microdeletions in Normal Tissues

(2012) Y. Shibata et al.   SCIENCE

Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome

(2012) Lesley A. Ogilvie et al.   Bioengineered

Plasmid Metagenome Reveals High Levels of Antibiotic Resistance Genes and Mobile Genetic Elements in Activated Sludge

(2011) Tong Zhang et al.   PLoS One

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Pathogenomics of the Virulence Plasmids of Escherichia coli

(2009) T. J. Johnson et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

DNAPlotter: circular and linear interactive genome visualization

(2008) T. Carver et al.   BIOINFORMATICS