Conserved phylogenetic distribution and limited antibiotic resistance of class 1 integrons revealed by assessing the bacterial genome and plasmid collection

PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

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

The Prevalence of Integrons as the Carrier of Antibiotic Resistance Genes in Natural and Man-Made Environments

(2017) Liping Ma et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Evolution of class 1 integrons: Mobilization and dispersal via food-borne bacteria

(2017) Timothy M. Ghaly et al.   PLoS One

ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database

(2016) Ying Yang et al.   BIOINFORMATICS

High Throughput Analysis of Integron Gene Cassettes in Wastewater Environments

(2016) Joao Gatica et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection

(2016) Li-Guan Li et al.   ISME Journal

Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing

(2016) K. Schmidt et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Identification and analysis of integrons and cassette arrays in bacterial genomes

(2016) Jean Cury et al.   NUCLEIC ACIDS RESEARCH

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments

(2016) Ivan Yevshin et al.   NUCLEIC ACIDS RESEARCH

Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken, and Human Feces

(2015) Liping Ma et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Integron diversity in marine environments

(2015) Justine Abella et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes

(2015) Bing Li et al.   ISME Journal

Global dissemination patterns of common gene cassette arrays in class 1 integrons

(2015) Sara Domingues et al.   MICROBIOLOGY-SGM

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Improved data analysis for the MinION nanopore sequencer

(2015) Miten Jain et al.   NATURE METHODS

GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes

(2015) Patricia P. Chan et al.   NUCLEIC ACIDS RESEARCH

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

PRISE2: Software for designing sequence-selective PCR primers and probes

(2014) Yu-Ting Huang et al.   BMC BIOINFORMATICS

Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

(2014) Michael R Gillings et al.   ISME Journal

Global antibiotic consumption 2000 to 2010: an analysis of national pharmaceutical sales data

(2014) Thomas P Van Boeckel et al.   LANCET INFECTIOUS DISEASES

Integrons: Past, Present, and Future

(2014) Michael R. Gillings   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

What is a resistance gene? Ranking risk in resistomes

(2014) José L. Martínez et al.   NATURE REVIEWS MICROBIOLOGY

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Rapid identification of high-confidence taxonomic assignments for metagenomic data

(2012) Norman J. MacDonald et al.   NUCLEIC ACIDS RESEARCH

A Trade-off between the Fitness Cost of Functional Integrases and Long-term Stability of Integrons

(2012) Irina Starikova et al.   PLoS Pathogens

Integron Involvement in Environmental Spread of Antibiotic Resistance

(2012) Thibault Stalder et al.   Frontiers in Microbiology

Classifying short genomic fragments from novel lineages using composition and homology

(2011) Donovan H Parks et al.   BMC BIOINFORMATICS

Database resources of the National Center for Biotechnology Information

(2011) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Distribution of Class 1 Integrons with IS26-Mediated Deletions in Their 3′-Conserved Segments in Escherichia coli of Human and Animal Origin

(2010) Fay E. Dawes et al.   PLoS One

INTEGRALL: a database and search engine for integrons, integrases and gene cassettes

(2009) A. Moura et al.   BIOINFORMATICS

Context-driven discovery of gene cassettes in mobile integrons using a computational grammar

(2009) Guy Tsafnat et al.   BMC BIOINFORMATICS

ACID: annotation of cassette and integron data

(2009) Michael J Joss et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Genome Project Standards in a New Era of Sequencing

(2009) P. S. G. Chain et al.   SCIENCE

Estimating the size of the bacterial pan-genome

(2009) Pascal Lapierre et al.   TRENDS IN GENETICS

Bad Bugs, No Drugs: No ESKAPE! An Update from the Infectious Diseases Society of America

(2008) Helen W. Boucher et al.   CLINICAL INFECTIOUS DISEASES

Gene cassettes encoding resistance to quaternary ammonium compounds: a role in the origin of clinical class 1 integrons?

(2008) Michael R Gillings et al.   ISME Journal

The Evolution of Class 1 Integrons and the Rise of Antibiotic Resistance

(2008) M. Gillings et al.   JOURNAL OF BACTERIOLOGY

Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns

(2008) J. R. Zaneveld et al.   MICROBIOLOGY-SGM

Phylogenetic classification of short environmental DNA fragments

(2008) Lutz Krause et al.   NUCLEIC ACIDS RESEARCH

Quantification of class 1 integron abundance in natural environments using real-time quantitative PCR

(2007) Simon A. Hardwick et al.   FEMS MICROBIOLOGY LETTERS