MinION Nanopore Sequencing Enables Correlation between Resistome Phenotype and Genotype of Coliform Bacteria in Municipal Sewage

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Rapid resistome mapping using nanopore sequencing

(2017) Eric van der Helm et al.   NUCLEIC ACIDS RESEARCH

Does antifouling paint select for antibiotic resistance?

(2017) Carl-Fredrik Flach et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Forensic SNP Genotyping using Nanopore MinION Sequencing

(2017) Senne Cornelis et al.   Scientific Reports

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

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Interconnected microbiomes and resistomes in low-income human habitats

(2016) Erica C. Pehrsson et al.   NATURE

Sensor histidine kinase is a β-lactam receptor and induces resistance to β-lactam antibiotics

(2016) Lu Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Ocean as a Global Reservoir of Antibiotic Resistance Genes

(2015) Stephen M. Hatosy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome analysis and in vivo virulence of porcine extraintestinal pathogenic Escherichia coli strain PCN033

(2015) Canying Liu et al.   BMC GENOMICS

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

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

(2015) Bing Li et al.   ISME Journal

Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes

(2015) Kim Judge et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Antibiotic resistance genes in the environment: prioritizing risks

(2015) Johan Bengtsson-Palme et al.   NATURE REVIEWS MICROBIOLOGY

IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis: Figure 1.

(2015) Bhavjinder K. Dhillon et al.   NUCLEIC ACIDS RESEARCH

Limited dissemination of the wastewater treatment plant core resistome

(2015) Christian Munck et al.   Nature Communications

Poretools: a toolkit for analyzing nanopore sequence data

(2014) N. J. Loman et al.   BIOINFORMATICS

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

What is a resistance gene? Ranking risk in resistomes

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

Fate of antibiotic resistance genes in sewage treatment plant revealed by metagenomic approach

(2014) Ying Yang et al.   WATER RESEARCH

Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences

(2014) Val F. Lanza et al.   PLoS Genetics

The Scourge of Antibiotic Resistance: The Important Role of the Environment

(2013) R. L. Finley et al.   CLINICAL INFECTIOUS DISEASES

Exploring Variation of Antibiotic Resistance Genes in Activated Sludge over a Four-Year Period through a Metagenomic Approach

(2013) Ying Yang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Metagenomic Profiles of Antibiotic Resistance Genes (ARGs) between Human Impacted Estuary and Deep Ocean Sediments

(2013) Baowei Chen et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota

(2013) Yongfei Hu et al.   Nature Communications

Parameters for accurate genome alignment

(2012) Martin C Frith 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

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Heavy metal driven co-selection of antibiotic resistance in soil and water bodies impacted by agriculture and aquaculture

(2012) Claudia Seiler et al.   Frontiers in Microbiology

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot et al.   GENOME RESEARCH

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

Call of the wild: antibiotic resistance genes in natural environments

(2010) Heather K. Allen et al.   NATURE REVIEWS MICROBIOLOGY

The large-scale organization of the bacterial network of ecological co-occurrence interactions

(2010) Shiri Freilich et al.   NUCLEIC ACIDS RESEARCH

Combined Inactivation of lon and ycgE Decreases Multidrug Susceptibility by Reducing the Amount of OmpF Porin in Escherichia coli

(2009) V. Duval et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora

(2009) M. O. A. Sommer et al.   SCIENCE

The occurrence of antibiotics in an urban watershed: From wastewater to drinking water

(2009) A.J. Watkinson et al.   SCIENCE OF THE TOTAL ENVIRONMENT