Global transmission of broad-host-range plasmids derived from the human gut microbiome

Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems

(2021) Christine He et al.   Nature Microbiology

Bacteria have numerous distinctive groups of phage–plasmids with conserved phage and variable plasmid gene repertoires

(2021) Eugen Pfeifer et al.   NUCLEIC ACIDS RESEARCH

PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets

(2021) Léa Pradier et al.   BMC BIOINFORMATICS

SCAPP: an algorithm for improved plasmid assembly in metagenomes

(2021) David Pellow et al.   Microbiome

Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform

(2020) Christian Munck et al.   Nature Communications

Large-scale network analysis captures biological features of bacterial plasmids

(2020) Mislav Acman et al.   Nature Communications

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

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

mMGE: a database for human metagenomic extrachromosomal mobile genetic elements

(2020) Senying Lai et al.   NUCLEIC ACIDS RESEARCH

Tracking of Antibiotic Resistance Transfer and Rapid Plasmid Evolution in a Hospital Setting by Nanopore Sequencing

(2020) Silke Peter et al.   mSphere

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

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

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

(2019) Yuanqiang Zou et al.   NATURE BIOTECHNOLOGY

Plasmid detection and assembly in genomic and metagenomic datasets

(2019) Dmitry Antipov et al.   GENOME RESEARCH

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

(2019) Zhencheng Fang et al.   GigaScience

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research

(2019) M. Poyet et al.   NATURE MEDICINE

A marine plasmid hitchhiking vast phylogenetic and geographic distances

(2019) Jörn Petersen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

OUP accepted manuscript

(2018)   BIOINFORMATICS

Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae

(2018) M Rozwandowicz et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

(2018) Pawel S Krawczyk et al.   NUCLEIC ACIDS RESEARCH

VFDB 2019: a comparative pathogenomic platform with an interactive web interface

(2018) Bo Liu et al.   NUCLEIC ACIDS RESEARCH

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

IncFII plasmid carrying antimicrobial resistance genes in Shigella flexneri: Vehicle for dissemination

(2018) Dhiviya Prabaa Muthuirulandi Sethuvel et al.   Journal of Global Antimicrobial Resistance

DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets

(2017) Julio Rozas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transfer and Persistence of a Multi-Drug Resistance Plasmid in situ of the Infant Gut Microbiota in the Absence of Antibiotic Treatment

(2017) Heidi Gumpert et al.   Frontiers in Microbiology

Recycler: an algorithm for detecting plasmids fromde novoassembly graphs

(2016) Roye Rozov et al.   BIOINFORMATICS

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

A reference gene catalogue of the pig gut microbiome

(2016) Liang Xiao et al.   Nature Microbiology

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

popart: full-feature software for haplotype network construction

(2015) Jessica W. Leigh et al.   Methods in Ecology and Evolution

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

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

(2014) Tue Sparholt Jørgensen et al.   PLoS One

Broad host range plasmids

(2013) Aayushi Jain et al.   FEMS MICROBIOLOGY LETTERS

Genomic evolution and transmission ofHelicobacter pyloriin two South African families

(2013) Xavier Didelot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

(2012) John H Morris et al.   BMC BIOINFORMATICS

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

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

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Helicobacter pylori genome evolution during human infection

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

The Human Gut Microbiome: Ecology and Recent Evolutionary Changes

(2010) Jens Walter et al.   Annual Review of Microbiology

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH